Field of Science

Why Is Plagiarism Bad?

A question has been going through my head, inspired by two unrelated happenings. The first is the deplorable aetosaur scandal that has been making blogging news. The second is that Jack and I are going to see a performance of Richard III this evening. What do Spencer Lucas and William Shakespeare have in common? The answer is that both of them have been accused of plagiarism.

Whether William Shakespeare actually plagiarised his works in detail remains a debatable question (see here, here and here, for instance), but one could certainly argue that Shakespeare did not invent much in the way of original plot lines. Fans of Shakespeare would nevertheless reply that even if that were true, the skill with which Shakespeare built on and improved his original sources surely makes up for his initial "borrowing".

The point I am considering is that our definition of what counts as "plagiarism" seems much broader now than it once was. I'm not referring specifically to the Lucas case in any way here - if the accusations are true, then that probably counts as unethical whatever period you look at it from. Besides, the standards of science are a little different from those of literature. It's just that the question of "what is plagiarism?" has been on my mind as a result of the case.

Herman Melville's Moby-Dick, or The Whale and Edgar Allen Poe's The Narrative of Arthur Gordon Pym of Nantucket were two books that retained their popularity and influence despite large sections of them being derived from other works. For instance, Poe lifted several passages out of Benjamin Morrell's A Narrative of Four Voyages, without even correcting typos. How were Poe and Melville able to get away with it?

One possible explanation that occurred to me was that maybe such extracts were more tolerated in the past was because plagiarism was actually harder to get away with in the past. The pool of authors and readers would have been much smaller in the 1800s than it is now, and as such, the chance that a reader would be familiar with a given source work would have been much higher. Did Poe feel able to draw from Morrell without the need to indicate he was doing so because he felt that most of his readers would have read Morrell and recognised his borrowed passages as such themselves? Whereas in the modern day and age, so many thousands if not millions of pieces of text are floating around out there that it would potentially be much easier to find some obscure source and pass off the work therein as your own. Does increased potential to get away with plagiarism mean that penalties have become higher to try and deter people from trying their luck? What do people out there think?

Circus of the Spineless

The latest edition of Circus of the Spineless, the monthly invertebrate blog carnival, is up at A DC Birding Blog.

Do I Need a Makeover?

I've been getting a few complaints lately about the colour-scheme I've been using - apparently, some people find the combination of white lettering on a black background too hard to read. Therefore, I'm running something of an experiment - I've changed the template over to black on white, and I'll see if it makes a significant difference to readership over the next few weeks. If not, I may go bacmk to the old style. Because personally, I liked it better.

Bitch and Moan, Moan and Bitch

I'd advise ignoring this post. It's just going to be me carping on about a few things that have come up lately that have been occupying my mind, but aren't really worth a post on their own, because, really, all it's going to be is bitching and moaning. I recommend you go read about wierd crustacean parasites, or cannibal algae, or bipedal adaptations in fossil artiodactyls, or something. They'll be better than this drek.

One of the big news items yesterday in the biology world was the release of the much-hyped Encyclopedia of Life (be warned that the link may have problems - the site is currently suffering from an overload of traffic as quite literally millions of people try to get access at once). One certainly can't fault the site for a lack of ambition - the EoL aims to be nothing less than a source of information for every single thing known about every single species of organism on the planet. So when I admit that I found my experience browsing through the first release of the site underwhelming, I have to add the caveat that it was probably doomed to be underwhelming to at least some degree. After all, the site itself estimates some 1.8 million named species, and new species continue to be published at the rate of hundreds per day. To a certain extent, we should be holding off on criticism now and seeing how the site develops over the next few years. Nevertheless, there are some notable quibbles - Rod Page covered a lot of them. The most significant quibble, of course, but the one to which my caveat applies the most, is that at the moment there just isn't that much info on most species pages. Lots of pretty pictures, but not very much actual info. This is something that can only be corrected over time, of course, but it does lead to my major problem with the site - how will that information be added? At the moment, EoL only presents information that has been authenticated by experts, and Carl Zimmer hits on the exact problem with this when he points out that there just aren't enough experts to authenticate information quickly enough. It has been exactly this problem that has hindered the Tree of Life project to some degree. Remember, for 1.8 million species, if a new species page was put up every day, it would take a little under 5000 years to get them all. I really feel that a Wikipedia type approach would be more appropriate in this case. True, Wikipedia can theoretically suffer from incorrect information being put up by uninformed editors, but in practice a lot of major errors are caught and corrected pretty early (and, of course, Wikipedia covers a lot more topics that EoL, and most of the real problems occur in politicised areas that EoL wouldn't cover). A recent article in Slate claims that the vast majority of significant edits in Wikipedia are actually made by only a small percentage of users - the Slate article felt that this was a problem for Wikipedia, but it would probably be exactly what EoL wants to meet its desired combination of authority and range of information. Allowing readers to edit directly would also mop up minor errors that I caught in browsing, like Cafeteria roenbergensis being abbreviated to C. Roenbergensis (that species name shouldn't be capitalised) and non-italicised genus names on the Chordata page.

The information for each species page is divided into sections such as "Overview" and "Description", and when the page is loaded only one section appears, along with a menu that allows you to click through to other sections. That's all well and good for species that have vast amounts of information available, because readers will not have to scroll through tons of information they may not be interested in to find what they want. It is, however, rather annoying when a species has very little information. Many of the pages may have only a sentence or two for each section and it takes some time to click through to see them all. Could there possibly be some way for all sections to appear at once when the total article length would not be very long? The layout of the text sections of the pages has some issues as well - the page is divided into three equal-sized columns - the navigation menu, the information section and a right-hand panel suggesting alternative pages to look at. The result is that the actual article appears cramped and crammed. Rod Page also mentioned the issue of no links in the article itself. If another taxon is mentioned in an article, it would be helpful if clicking on the name linked through to the appropriate page. This is particularly significant because, for instance, the page on the protist Cafeteria roenbergensis actually incorporates a lot of information on related taxa. Without a link from the pages for those taxa to Cafeteria, browsers may remain completely unaware that the information is even available.

The whole Aetogate thing is continuing to depress us all. A committee was called to review Lucas' behaviour in the whole thing, and decide if he's been a bad boy or not. So they get in two 'independent' researchers to look things over - who happen to be close associates of Lucas! What really makes things irritating, though, is that one of the 'independent advisors', Norman Silberling, actually writes a letter that gets reprinted in the local newspaper, the Albuquerque Journal, in which he declares his total faith in Lucas' good conduct, and does so before the committee even meets! Seriously, what the fuck? I don't think there's much I can add to the situation that hasn't been said before by more competent people, so I'll direct you to what has been said by Janet Stemwedel, Rebecca Hunt, Brian Switek and Julia Heathcote. And, of course, you can keep an eye on the whole sad and ugly process via Mike Taylor.

There was more I was going to write about, but I've wasted enough of your and my time as it is. Sorry.

Linnaeus' Legacy Time

In a week's time, I'll be hosting the fifth edition of Linnaeus' Legacy, the monthly taxonomy and biodiversity carnival. I've been seeing some good taxonomically-oriented posts around the blogosphere this past month, so I know there's plenty out there to include. If you want to stake your claim to a part of the fun, get your links in to me by the 4th of March!

The Dinosaur Diagnosis Wars

Zach Miller at When Pigs Fly Returns has offered up a couple of original diagnoses of dinosaur species to be guessed at, here and here. So far I've gotten him on both of them, so I thought it only fair to offer my own up in return. So, Zach, anyone, can you identify what beasty made its debut under these words:

The vertebrae, and the bones of the limbs and of the feet, are so much like the corresponding parts of the typical Stegosaurus from the Jurassic, that it would be difficult to separate the two when in fragmentary condition, as are most of those from the later formation. The latter forms, however, are of larger size, and nearly all the bones have a peculiar rugosity, much less marked in the Jurassic species. In the form here described, this feature is very conspicuous, and marks almost every known part of the skeleton...

The top of the skull... is thick and massive, and strongly rugose.

This skull as a whole must have had at least fifty times the weight of the skull of the largest Sauropoda known, and this fact will give, some idea of the appearance of this reptile when alive.

In the interests of full disclosure, I've omitted a paragraph or two there, but only because if I had included the missing section it would have all been too easy. And if I'm to be labelled "a right bastard", then I feel that I must do what I can to maintain the honorific.

Boneyard #14

The newest edition of the Boneyard is up at Self-Designed Student. Lots of dinosaurs this time around, but the nomenclatorial highlight has to be the fantastically-named giant frog Beelzebufo.

Barklice and Booklice and Such

Psocoptera is arguably the least deservedly obscure of the obscure insect orders. They're not uncommon - there's a reasonable chance that you'll have seen one in your life. You probably squashed it without giving much thought to what it was. And yet, so obscure is this order of insects that there isn't even a good vernacular name for the group. Psocoptera are minute insects (usually only a couple of millimetres long) that generally live among bark and litter, feeding on fungi. Some wingless species can be found in houses (where you might have seen one) and feed on such delicacies as dust or the glue used in book bindings, leading to their being known as booklice. The tree-living forms are sometimes referred to as barklice in comparison to booklice. Most entomologists that I know simply refer to the group as psocids, and that's exactly what I'm going to do.

Technically speaking, 'Psocoptera' is a paraphyletic group. The Phthiraptera, the true lice*, are derived from within the psocids. At the moment, things seem to be going through a transitional phase, with many authors dropping the paraphyletic 'Psocoptera' for the name Psocodea, which refers to the total group of psocids and lice. The 'Psocoptera' are divided into three suborders, the Trogiomorpha, Psocomorpha and Troctomorpha, the Phthiraptera being properly speaking a subgroup of the last. A representative of the second group, the psocomorph Blaste (photo from TOLWeb), can be seen at the top of this post, and it's the Psocomorpha that I'm looking at today.

*And holders of what is probably the worst insect order name of all to pronounce.

With over 3500 species, the Psocomorpha are generally regarded as the largest of the psocid suborders, though the Troctomorpha could give them a run for their money once the Phthiraptera are taken into account. We should probably be careful about making definite statements about this - because of their neglected nature, new species and sometimes even families of psocids continue to appear in the literature at a respectable rate. At the moment, though, it is a psocomorph that holds the honour of being probably the only invertebrate to get its picture plastered over Tetrapod Zoology, due to the nomenclatural issues that have arisen from the similarity in names of the psocid Caecilius and the amphibian Caecilia. The photo above is the one featured in Tet Zoo, and shows an identified member of the Caeciliusidae.

Most Psocomorpha are dwellers on bark or rocks. One group, the Caeciliusoidea, inhabits living foliage. Adults may be winged or wingless - many species have both forms. Many psocids cluster as nymphs - the photo above (from here*) shows one such congregation - and spin protective webs, but this is taken to the extreme in the genus Archipsocus. Archipsocus species form large colonies, and may build webs large enough to obscure tree-trunks, as can be seen in the picture below (from here). As with Embioptera, these colonies appear to be conglomerations of convenience, and there is no real social behaviour. Like aphids, Archipsocus may go through multiple generations in a summer, and the colony will contain individuals at all stages of development, both winged and wingless forms (Mockford, 1957). Once winter arrives, the colony breaks down and disperses, the survivors diapausing until the spring when they will start new colonies.

*This page also records a fantastic common name for psocids - "bark cattle", apparently because the nymphs move like a herd when disturbed.

Molecular and morphological data are mostly in agreement that the Psocomorpha can mostly be divided between four infraorders, the Psocetae, Homilopsocidea, Epipsocetae and Caeciliusetae (Johnson & Mockford, 2003; Yoshizawa, 2002). Both studies also agreed in placing Archipsocus outside these groups, as the basalmost member of the Psocomorpha. Unfortunately, beyond the bare morphology, information about most psocid groups seems to be few and far between, and there is a great deal about the order that we have yet to know.


Johnson, K. P., & E. L. Mockford. 2003. Molecular systematics of Psocomorpha (Psocoptera). Systematic Entomology 28: 409-416.

Mockford, E. L. 1957. Life history studies on some Florida insects of the genus Archipsocus (Psocoptera). Bulletin of the Florida State Museum - Biological Sciences 1 (5): 254-274.

Yoshizawa, K. 2002. Phylogeny and higher classification of suborder Psocomorpha (Insecta: Psocodea: ‘Psocoptera’). Zoological Journal of the Linnean Society 136: 371-400.

Bird Carnival

The bird carnival I and the Bird has been up for a couple of days now at Living the Scientific Life (Scientist, Interrupted). My apologies for the late link, but I'm sure the posts are timeless!

The Secret of Y-Larvae

Deep Sea News has some neat pictures of a rhizocephalan for you to look at. Rhizocephalans are definitely one of the stranger parasitic crustaceans, with an almost fungal-looking structure that spreads through their crustacean host, and its machiavellian hijacking of the host's reproductive system for its own ends. Seriously, take a look, though you may want to wait a little if you've just had breakfast.

Rhizocephalans are actually fairly close relatives of barnacles, both of them belonging to a group of crustaceans called Thecostraca. Though the different thecostracan subgroups are very different in adult morphology, they are united by their similar larval morphology. As well as the standard crustacean nauplius larva, thecostracans have an additional larval stage known as a cypris larva, a motile stage with specialised sensory structures that the larva uses to seek out a suitable host or substrate to attach to and develop into the adult. As well as barnacles and rhizocephalans, the Thecostraca includes another few small crustacean groups, the Ascothoracida, the Acrothoracica, and the Facetotecta. Acrothoracica or burrowing barnacles burrow into hard substrates such as mollusc shells, other free-living barnacles, corals or limestone. Ascothoracida are minute parasites of molluscs and other marine animals. But I thought I'd reply to Deep Sea News' post by writing something on the last group, the Facetotecta.

The infraclass (or subclass, or whatever you want to call it) Facetotecta contains a single genus, Hansenocaris. Despite being discovered well over a hundred years ago, Hansenocaris remains, in many regards, very little known. The main thing we don't know about Hansenocaris is what it actually looks like. So far, this group of thecostracans is known only from distinctive larvae referred to as "y-larvae"* - the adult form is a complete mystery. The most distinctive feature of the y-larva is its large univalved head shield, whose faceted nature is the source of the name "Facetotecta". Both nauplius and cypris stages have been collected and well-studied, but that's as far as it goes (the photo above, from Høeg & Kolbasov, 2002, shows an SEM of a y-cypris). Certain features of the cypris larva's morphology suggest that, like most other thecostracan subgroups, Hansenocaris becomes parasitic at maturity (as I noted in a comment at Deep Sea News, the non-parasitic barnacles are actually the odd ones out here), but no-one knows on what.

*Why "y-larvae"? That I couldn't tell you, but according to Ponomarenko (2006) the name dates back to their original description by Hansen in 1899.

One suggestion that has been made is that y-larvae may fit into the little-known sexual phase of the life cycle of the Tantulocarida (Ponomarenko, 2006). Tantulocarids are another group of ectoparasitic crustaceans (living on other crustaceans) that are believed to be the sister group of the thecostracans, and are another group of animals that contend for the title of "almost too stupidly bizarre to be believable". The tantulocarid life cycle is unique in lacking the usual moulting stages of all other crustaceans - instead, the mature adult actually develops within the attached parasitic tantulus larva (Boxshall & Lincoln, 1997). Check out the diagram below from Boxshall & Lincoln (1997) showing this process. Personally, I have a hard time thinking of this as development from larva to adult (despite all the papers describing it as such) - it looks more like a reproductive process where the adult develops asexually by a sort of internal budding from the tantulus. Reproduction in tantulocarids is either asexual or sexual (Huys et al., 1993) - in the asexual phase, the tantulus larva swells into a sac filled with developing eggs that are believed to be retained to hatch out into fully-developed tantulus larvae. In the sexual phase, as shown, the larva gives rise to a single mature adult. What happens once the mature male is released into the world is unknown, but as the male lacks functional mouthparts it undoubtedly dies after finding a mate. The sexual female described by Huys et al. (1993) was still attached to the host via the umbilicus, the nutrient-delivering tube you can see in fig. 26 below, and it seems possible that it remains so attached for all or most of its life, continuing to draw nutrients from the host to nurse its developing eggs. Huys et al.'s female, unfortunately, was carrying only immature eggs, so whether the eggs are retained to the tantulus stage as in the parthenogenetic phase, or hatch into more standard nauplius larvae, remains unknown.

This period of ignorance does give a window for identifying y-larvae with tantulocaridans. The idea is also not without phylogenetic merit - tantulocaridans are regarded as the sister group to Thecostraca, while most phylogenetic analyses place Facetotecta as fairly basal thecostracans. However, the identification does not seem to be well-accepted*. Most significantly, the tantulus larva of Tantulocarida has no sign of lattice organs. Lattice organs are specialised sensory organs on the carapaces of thecostracan cypris larvae, including y-larvae, that are believed to function in helping the cypris find a suitable substrate for attachment** (Høeg & Kolbasov, 2002). It would be surprising if sexually-produced dispersing larvae of tantulocaridans were to possess lattice organs but asexually-produced dispersing larvae (that surely would have just as much use for them) did not.

*Google Books can be very frustrating. The Google Book preview for Scholtz (2004) allows me to read that "there are strong arguments against a tantulocaridan-facetotectan relation" at the end of page 209, but then page 210, where I would have undoubtedly been told about said arguments, is not part of the preview. Gah!

**However, Lange & Schram (2002) identified apparent sensory structures on the carapace of fossil thylacocephalans as possibly homologous to lattice organs, despite the believed free-living nature of thylacocephalans. Mind you, the strange morphology of Thylacocephala was so highly derived that it's pretty much anyone's guess just what they were up to.

Which brings us firmly back to square one. The adult form of Hansenocaris remains one more example of just how little we know of the marine environment. It's out there somewhere - the question is where.


Boxshall, G. A., & R. J. Lincoln. 1987. The life cycle of the Tantulocarida (Crustacea). Philosophical Transactions of the Royal Society of London Series B - Biological Sciences 315 (1173): 267-303.

Høeg, J. T., & G. A. Kolbasov. 2002. Lattice organs in y-cyprids of the Facetotecta and their significance in the phylogeny of the Crustacea Thecostraca. Acta Zoologica 83: 67-79.

Huys, R., G. A. Boxshall & R. J. Lincoln. 1993. The tantulocaridan life cycle: the circle closed? Journal of Crustacean Biology 13 (3): 432-442.

Lange, S., & F. R. Schram. 2002. Possible lattice organs in Cretaceous Thylacocephala. Contributions to Zoology 71 (4): 159-169.

Ponomarenko, E. A. 2006. Facetotecta - unsolved mystery of marine biology. Russian Journal of Marine Biology 32 (Suppl 1): S1-S10.

Scholtz, G. 2004. Evolutionary Developmental Biology of Crustacea. CRC Press.

What is the Sound of One Mayfly Fossilising?

Actually, two mayflies. That is, unless they're not mayflies.

Krzeminski, W. & C. Lombardo. 2001. New fossil Ephemeroptera and Coleoptera from the Ladinian (Middle Triassic) of Canton Ticino (Switzerland). Rivista Italiana de Paleontologia e Stratigrafia 107 (1): 69-78.

The Triassic is apparently not a fantastic time, insect-wise. Fossil insects from the Triassic are fairly few and far between. Needless to say, this is really annoying, because it was probably a fairly significant time in insect evolution. The giant insects of the Palaeozoic were no more - instead, it was about this time that many of the modern insect orders stepped in to take their place (Grimaldi & Engel, 2005). This unfortunately brief paper by Krzeminski & Lombardo (2001) gives us just a couple of pieces of the puzzle, but it's debatable just what we can do with them.

First, the maybe-mayfly. Krzeminski & Lombardo described Tintorina from two specimens (unfortunately, while the name Tintorina triassica appears in the abstract, the name used in the body of the article is Tintorina meridensis - I'm not sure, but I think the latter would be the correct name). The holotype retains most of the body (the head is missing), two of the wings and a few bits of leg. The paratype is just a pair of wings and a fragment of body. Though fragmentary, this collection does not put us too badly off. A large percentage of insect fossil species are only known from the wings, and the pattern of venation therein is hence the most commonly used suite of characters for distinguishing taxa. Krzeminski & Lombardo assign Tintorina to a new family of Ephemeroptera. They cite the wing venation and the general body shape as their reason for doing so, but unfortunately do not note exactly which features of the venation they refer to. Features such as the absence of a humeral vein (a small vein near the base of the wing) indicate that, if Tintorina is related to Ephemeroptera, it must lie outside the crown group. The only author to specifically comment on Tintorina since seems to be Kluge (2004), who concurred in the overall similarity of venation with Ephemeroptera, but also noted a couple of significant differences. As a result, Kluge moved Tintorina to Pterygota incertae sedis.

Next, the beetle. Coleoptera fossils are known since the Lower Permian, but carry problems all of their own. Almost the entire early fossil record of beetles is composed of isolated elytra, which offer few diagnostic characters and which may be suspected of rampant homoplasy (Ponomarenko, 2002). While representatives of recent families or their close relatives have been described from early on, a lot of doubt must hang over the accuracy of these identifications. A classic example is the Triassic family Obrieniidae, originally identified as the earliest representatives of the weevils (Curculionoidea), but now regarded as merely convergent (Kuschel, 2003). In the case of Krzeminski & Lombardo (2001), they assign a single elytron to the genus Notocupes in the family Cupedidae. The Cupedidae survive to this day - an example of a living species (Tenomerga mucida) is shown at the top of the post in a photo from Wikipedia. Generally found in rotten wood, the are one of the few survivors of the basal (paraphyletic?) beetle suborder Archostemata, making them very interesting in understanding beetle evolution. The genus Notocupes (recently regarded as a synonym of Zygadenia by Ponomarenko, 2006) is a fossil genus known from Triassic to the Palaeocene - a really quite spectacular length of time, and, in light of the problems I've just mentioned, really worth a further look.


Kluge, N. 2004. The Phylogenetic System of Ephemeroptera. Springer.

Kuschel, G. 2003. Nemonychidae, Belidae, Brentidae (Insecta: Coleoptera: Curculionoidea). Fauna of New Zealand 45.

Ponomarenko, A. G. 2002. Superorder Scarabaeidea Laicharting, 1781. Order Coleoptera Linné, 1758. The beetles. In History of Insects (A. P. Rasnitsyn & D. L. J. Quicke, eds.) pp. 164-176. Kluwer Academic Publishers: Dordrecht.

Ponomarenko, A. G. 2006. [On the types of Mesozoic archostematan beetles (Insecta, Coleoptera, Archostemata) in the Natural History Museum, London]. Paleontologicheskii Zhurnal 2006 (1): 86-94 (transl. Paleontological Journal 40 (1): 90-99).

Another Non-missing Not-quite-link

Today's Nature has a significant article that I'd like to draw your attention to, but before I do I've got a complaint to make. One of the letters in today's Nature (Seeber, 2008) addresses the question of citations in online Supplementary Information. I've moaned before about the problems with online Supplementary Information for papers - most notably the issue of it becoming unavailable over time - and Seeber's letter gives me one more reason to dislike SI. Apparently, the various sources of citation rankings such as impact factors don't include citations that only appear in Supplementary Info. What really gets my goat, though, is that the editor of Nature states in a replying note that, "Supplementary information for Nature... does not usually contain references". This is simply not true.

The Supplementary Information for the paper I'm about to write on has a bibliography of 53 references. Saarela et al. (2007) included 13 supplementary references, as did Xu et al. (2007). Brandt et al. (2007) had 62. The SI for Bininda-Emonds et al. (2007) has 75 references. In fact, I haven't often seen a Supplementary Information file that hasn't included extra references, so if Nature has a policy of discouraging supplementary references, they're not doing a very good job of enforcing it.

Now that that little gripe is over and done with, on to the good stuff:

Moore, R.B., M. Oborník, J. Janouškovec, T. Chrudimský, M. Vancová, D. H. Green, S. W. Wright, N. W. Davies, C. J. Bolch, K. Heimann, J. Šlapeta, O. Hoegh-Guldberg, J. M. Logsdon & D. A. Carter. 2008. A photosynthetic alveolate closely related to apicomplexan parasites. Nature 451 (7181): 959-963. DOI: 10.1038/nature06635

After years of ignorance, we are slowly piecing together an understanding of the inter-relationships between the various groups of eukaryotes. In the process of doing so, researchers have confirmed some traditionally recognised groups, dismantled others, and recognised new groupings that were previously unsuspected. One well-supported group of protists that has emerged into the light is the Alveolata. Alveolates combine three superficially dissimilar groups - the ciliates, dinoflagellates and sporozoans - united by the possession of alveoli, flattened membrane-bound vesicles directly under the cell surface, supported by microtubules. Within the alveolates, it is also generally agreed that the dinoflagellates and sporozoans are more closely related to each other than to the ciliates.

The sporozoans are parasitic forms that include a number of significant pathogens such as Plasmodium, the cause of malaria, and Cryptosporidium. One of the interesting, relatively recent discoveries about this group of organisms was that some of them possess a remnant, colourless plastid (referred to as the apicoplast), which together with the presence of chloroplasts in the related dinoflagellates suggested a photosynthetic ancestor. Understanding the origin of apicoplasts has become particularly significant as it has been touted as a potential target in developing treatments for sporozoan infections that target the parasite without damaging the host.

Unfortunately, a direct connection between the apicoplast and the dinoflagellate chloroplast has remained largely theoretical. Not all sporozoans possess apicoplasts - only a particular clade (including coccidians and Plasmodium) does so, while other sporozoans such as gregarines and Cryptosporidium show no sign of them. Chloroplasts or chloroplast remnants are also absent in an assortment of alveolate flagellate taxa (such as Colpodella) that are regarded as falling within the dinoflagellate-sporozoan clade. Direct comparison of apicoplasts and dinoflagellate chloroplasts is pretty much impossible - apicoplasts have (unsurprisingly) lost all photosynthetic genes, while dinoflagellate chloroplasts have developed severe wierdnesses of their own where they have pretty much lost all genes except the photosynthetic ones*. As a result, researchers have been unable to entirely rule out the possible that sporozoans gained their plastids independently from dinoflagellates. This is where today's announced discovery comes in.

*And severely altered what little they have left. In fact, dinoflagellate genomes as a whole are wierd beyond all belief - they're the only eukaryotes to have lost histones, for instance. I have no idea why they're so strange.

Chromera velia is a small photosynthetic eukaryote, shown above in a photo from the News and Views section of Nature. It is generally immotile, though an internal(!) cilium is present at one end of the cell, and motile stages were seen briefly in old cultures. Reproduction was mainly by binary division - frustratingly, Moore et al. add "not restricted to binary division", but completely fail to explain what this means and how sexual reproduction occurred (if it occurred). In fact, the paper as a whole is frustratingly uninformative about the ultrastructure of Chromera*, being mostly dedicated to the molecular phylogeny of the new taxon relative to other alveolates.

*I mean, seriously, how can you refer to an internal cilium and not go further?

The molecular phylogeny quite strongly supports Chromera as more closely related to sporozoans than dinoflagellates, though less closely related to sporozoans than are colpodellids. The discovery of this photosynthetic member of the sporozoan line adds additional support to the idea that sporozoans are ancestrally photosynthetic.

However, this does not automatically mean that dinoflagellate and sporozoan plastids share a single origin, despite the authors' conclusions. Analysis of plastid genes gave conflicting results - psbA supported a dinoflagellate-Chromera grouping, but SSU rDNA did not. Alveolates have also been suggested to be closely related to the chromists, another group of mostly photosynthetic eukaryotes (including brown and golden algae and diatoms), in a larger grouping called 'chromalveolates'. The existence of the chromalveolate clade was first suggested by their mutual possession of chlorophyll c, a form of chlorophyll not found in any other organisms*. However, Chromera lacks chlorophyll c, and possesses chlorophyll a only, like the red algae from which chromalveolate plastids are derived.

*For those unfamiliar with the various chlorophylls, chlorophyll a is the ancestral form found in pretty much all chlorophyll-containing organisms. Chlorophyll b is found in green algae, land plants and organisms with green alga-derived plasmids, as well as a few Cyanobacteria. Chlorophyll c, as I've said, is found in chromists and dinoflagellates.

The authors of Chromera assume that this indicates a loss of chlorophyll c in the ancestor of Chromera, but I would say that this is too strong a conclusion. The possibility that the sporozoan + Chromera ancestor gained its chloroplast independently from the dinoflagellate ancestor remains alive and well, and, as always, we need to look further into this question.


Bininda-Emonds, O. R. P., M. Cardillo, K. E. Jones, R. D. E. MacPhee, R. M. D. Beck, R. Grenyer, S. A. Price, R. A. Vos, J. L. Gittleman & A. Purvis. 2007. The delayed rise of present-day mammals. Nature 446: 507-512 (SI here).

Brandt, A., A. J. Gooday, S. N. Brandão, S. Brix, W. Brökeland, T. Cedhagen, M. Choudhury, N. Cornelius, B. Danis, I. De Mesel, R. J. Diaz, D. C. Gillan, B. Ebbe, J. A. Howe, D. Janussen, S. Kaiser, K. Linse, M. Malyutina, J. Pawlowski, M. Raupach & A. Vanreusel. 2007. First insights into the biodiversity and biogeography of the Southern Ocean deep sea. Nature 447: 307-311 (SI here).

Saarela, J. M., H. S. Rai, J. A. Doyle, P. K. Endress, S. Mathews, A. D. Marchant, B. G. Briggs & S. W. Graham. 2007. Hydatellaceae identified as a new branch near the base of the angiosperm phylogenetic tree. Nature 446: 312-315 (SI here).

Seeber, F. 2008. Correspondence: Citations in supplementary information are invisible. Nature 451 (7181): 887.

Xu, X., Q. Tan, J. Wang, X. Zhao & L. Tan. 2007. A gigantic bird-like dinosaur from the Late Cretaceous of China. Nature 447: 844-847 (SI here).

Tarantulas sans Tarantella

It's interesting how different people perceive levels of risk. Someone once asked how I could be completely unafraid of spiders, but be extremely nervous around cars (I am - a friend of mine once banned me from riding in the passenger seat when she was driving, because the sight of my knuckles turning white as I gripped onto the handlebar would make her nervous). I asked him in return how I could possibly be otherwise - hardly anyone is ever seriously hurt by a spider, but cars kill large numbers of people on a regular basis. The point of that little anecdote, in case you were wondering, is to introduce a family of spiders that have provided stock horror film fodder for years, but are widely known to be fairly harmless - the Theraphosidae.

Theraphosidae are a family of large spiders found mostly in ex-Gondwanan landmasses - South America, Africa, India and Australia, as well as in south-east Asia. These are the spiders best known as bird-eating spiders or tarantulas, though the name "tarantula" originally applied to a member of a quite different family of spiders, the European wolf spider Lycosa tarantula. The photo at the top of the post (from here) shows an Australian species of Selenocosmia. The photo just above this paragraph (from Tarantulas from Uruguay*) of Theraphosa leblondi gives a good idea of the size some theraphosids reach. Theraphosidae include the largest living spiders - indeed, since the Carboniferous Megarachne was reidentified as an eurypterid, modern Theraphosidae include the largest spiders known to have existed ever.

*I rather enjoyed the Tarantulas from Uruguay page, but if you're at work you might want to be forewarned that the page does play music at you.

Theraphosidae belong to the group of spiders known as mygalomorphs. Spiders can be divided into three major groups - liphistiomorphs, mygalomorphs and araneomorphs. Liphistiomorphs are a small group found in eastern Asia that represent the sister group of all other spiders, and can be distinguished from other spiders by their retaining an obviously segmented abdomen. The other two groups of spiders can most easily be distinguished by their chelicerae (fangs). Mygalomorphs retain the more primitive condition of having the fangs directed straight up and down, and so are only able to stab down with them. Araneomorphs, by far the larger and more diverse of the three groups, have the fangs directed towards each other and are able to pinch prey or attackers between the chelicerae (the Wikipedia page for Araneomorphae has a good pair of photos showing the difference). Mygalomorphs are mostly relatively large spiders (there are a few exceptions). They also tend to be far less sexually dimorphic than many araneomorphs, with relatively little difference between males and females.

While the bites of Theraphosidae are apparently not particularly notable as far as humans are concerned, of more concern for people handling tarantulas is the presence on the abdomen of many South American species of urticating hairs - specialised hairs with minute barbs that can break off and irritate the skin of any threatening predators. Members of the subfamily Theraphosinae can even propel the hairs directly at a threat by rubbing the legs against the abdomen. Members of two genera of theraphosids have also been recorded to incorporate shed urticating hairs into the silk of egg-sacs, which was demonstrated to increase the defense offered by the egg-sac against insect egg predators (Marshall & Uetz, 1990).

The South American Avicularia metallica (image from here).

Many species of Theraphosidae are popular as pets, and females may live for up to thirty years in captivity (males, in contrast, do not survive long after mating). Unfortunately, while pet individuals of the more popular species such as the red-kneed tarantula (Brachypelma smithi) are generally captive-bred, a substantial market (in many places, such as Australia, a largely illegal market) exists in wild-caught specimens, especially of rare and unusual species. Many theraphosid species have very limited ranges, and are severely threatened by collection for the pet trade, and I have been informed that at least some Australian species have actually become extinct due to over-collection. This is especially tragic as a large proportion of the Australian theraphosid population remains undescribed, necessitating a race against time to recognise their diversity before the opportunity to protect it is lost forever.


Marshall, S. D., & G. W. Uetz. 1990. Incorporation of urticating hairs into silk: a novel defense mechanism in two Neotropical tarantulas (Araneae, Theraphosidae). Journal of Arachnology 18: 143-149.

The Boneyard #13

The Boneyard is the blog carnival celebrating palaeontology - the latest issue has appeared at Greg Laden's Blog.

Funnily enough, Greg seems to have mistaken my previous post on Podosphaeraster for a fossil post. Nope - Podosphaeraster is alive and well and doing who-knows-what in the modern ocean.

Mystery Animal for Today

Take a close look at the photo above. What kind of animal do you think this is? [The photo comes from here, but don't look there just yet, because that would be cheating.]

Some of the more observant among you may have noticed the five rays visible on the animal, and so you would have correctly decided that this is an echinoderm, seen from the underside. Echinoderms are the phylum of marine animals that includes crinoids (sea lilies and feather stars), asteroids (sea stars or starfish), ophiuroids (brittle stars), echinoids (sea urchins) and holothuroids (sea cucumbers). The five rays are the ambulacra - furrows lined with the tube feet that the echinoderm uses for walking on, or for passing food particles to the central mouth. Before I reveal exactly what kind of echinoderm this is, though, I'll show you another photo of the same specimen (from the same site) seen from the side:

By now, it should be pretty obvious which of the five living classes of echinoderms this is. So if you guessed "starfish"* - you're absolutely right. This specimen is, in fact, the type specimen of Podosphaeraster toyoshiomaruae Fujita & Rowe, 2002. Podosphaeraster is an extremely unusual asteroid known from the western Pacific and north-east Atlantic that has abandoned the typical star-shape of most members of its class, and adopted a near-spherical form much more similar to that of an echinoid. If you were to look closely at the specimen, you would be able to see a difference from a typical echinoid in that the ambulacral furrows only go halfway up the side of the sphere, rather than all the way up as in echinoids.

*Kevin Zelnio is going to kill me for calling it a starfish instead of a sea star. Tough.

The way in which Podosphaeraster has evolved its unusual form is relatively simple. The development of the plates that normally form the dorsal (aboral) surface of the flattened star has been greatly reduced relative to those that form the ventral (oral) surface. The reasons why this unusual morphology has evolved in Podosphaeraster, however, are unknown. Though five species have been described to date, specimens of Podosphaeraster are few and far between. All species are small (the largest specimens are little over a centimetre in diameter) and there is evidence that they live in habitats that are not conducive to easy collecting - among sponges or rocky ground in depths of 85 - 615 m. It may be adapted to living in cracks or crevices in these habitats.

For all its unusualness, Podosphaeraster is not unique. A fossil family of asteroids, the Sphaerasteridae, also developed a similar globose form by the reduction of the aboral surface. Also, Smith (1997) suggested that echinoids could have also evolved from a star-like ancestor in just this way. If true, what might seem an interesting but inconsequential oddity in the asteroid world could actually be very significant in understanding how another of the major modern animal groups came into being.


Fujita, T., & F. W. E. Rowe. 2002. Podosphaerasteridae fam. nov. (Echinodermata: Asteroidea: Valvatida), with a new species, Podosphaeraster toyoshiomaruae, from southern Japan. Species Diversity 7: 317-332.

Smith, A. B. 1997. Echinoderm larvae and phylogeny. Annual Review of Ecology and Systematics 28: 219-241.

On Hybrid Birds

Fuller, E. 1995. The Lost Birds of Paradise. Swan-Hill Press.

The 19 "lost" birds of paradise that Errol Fuller describes in this book are forms that are mostly only known from very few specimens, often with very little supporting information. What makes them "lost", however, is that despite all but one of them being described as new species, all of them were later reinterpreted as hybrids between better-known species. Fuller's motivating question is whether these specimens are indeed hybrids, or represent valid species that might occupy unknown restricted ranges somewhere in the depths of New Guinea, or may perhaps have slipped into extinction without ever getting the recognition they deserved.

Most of the specimens reached Europe through the plume trade. Specimens of birds of paradise were purchased from native collecters and then shipped back to the West for use in the fashion industry (the first country to ban the import of birds of paradise for plumes, according to Fuller, was the US in 1913, a development that probably had less to do with the developing conservation movement than with the increasing unfashionability of wearing plumes*). As a result, the available collection data on most specimens is decidedly hazy - few bear more specific information than "Dutch New Guinea" (the western part of New Guinea that is now controlled by Indonesia). Even if a more specific locality is recorded, it is often unreliable - specimens could be passed through a number of different native tribes before eventually reaching the European traders. Throughout the book, we get introduced to many of the figures involved in the collection and study of these mystery birds.

*To add further complexity, a major factor in the decline of popularity of plumes was actually the rise in popularity of the motor-car - ornate plumed hats being decidedly impractical for wearing in open-topped cars.

'Paradisaea mirabilis', a possible hybrid of Paradisaea minor (lesser bird of paradise) and Seleucidis melanoleuca (twelve-wired bird of paradise). 1902 lithograph by Bruno Geisler.

Throughout Fuller's book, we get introduced to many of the personages involved in the collection and study of the specimens (including the spectacularly named Captain Neptune Blood*). A significant number passed through the collection of Lord Walter Rothschild, a somewhat eccentric enthusiast who amassed one of the world's largest private natural history collections (Darren Naish wrote a piece two years ago on Rothschild and his unusual enthusiasm for cassowaries), though many of Rothschild's bird of paradise specimens were included in the collection he was blackmailed into selling to the American Museum of Natural History**. The "hybrid" specimens were largely identified as such in 1930 by Erwin Stresemann. Fuller accuses Stresemann of overzealousness in embracing his hybrid theory of origin for "species" known only from one or two specimens, essentially assuming from the start that all such species must be hybrids of known species and identifying "parents" from the available options no matter how poorly supported.


**Probably not, I hasten to add, by the American Museum of Natural History.

'Diphyllodes gulielmitertii', almost certainly a hybrid between Diphyllodes magnificus and Cicinnurus regius. Unlike most of the other forms described by Fuller, this hybrid occurs fairly commonly, with more than two dozen known specimens. Lithograph by J. Gould and W. Hart.

Unfortunately, many of Fuller's reinterpretations of the supposed hybrids end up falling a little flat. Fuller accepts a hybrid origin for some forms, refutes it for others, but in many cases it is debatable whether his interpretations are any better than Stresemann's. Because all Fuller has to go on is examination of specimens, most of his arguments for valid species status amount to little more than replying to Stresemann's statement that "Species A has features intermediate between those of B and C, and is therefore a hybrid between the two" with "No it doesn't, so it isn't". In two cases where Fuller does accept hybrid status, 'Loborhamphus ptilorhis' and 'Lamprothorax wilhelminae', the reasons for linking them to their supposed parents seem decidedly unconvincing (which, of course, does not eliminate the possibility that they could still be hybrids between other species), while 'Cicinnurus lyogyrus', which Fuller hesitatingly accepts as a hybrid of the king bird of paradise (Cicinnurus regius) and the magnificent bird of paradise (Diphyllodes magnificus) seems more likely to be simply an aberrant variant of Cicinnurus regius. In contrast, 'Janthothorax bensbachi', which Fuller suggests is a valid species, seems more likely to be a hybrid. Probably DNA analysis of the specimens would be the only way to convincingly decide the question one way or another - Fuller suggests this would be difficult because the close relationships of the parent species would make results unconvincing, but resolution of molecular analyses has decidedly improved since 1995. The main barrier would be that DNA extraction from museum specimens, especially ones that have been in storage since the 1800s (and were probably not exactly fresh when they first reached the museum) is a difficult process, with little guarantee of success.

Loborhamphus nobilis, regarded by Stresemann (1930) as a hybrid between Paradigalla carunculata and Lophorina superba, but by Fuller as a probable valid species. Unlike the other bird of paradise species mentioned in this post, the less sexually dimorphic Paradigalla species are not polygamous breeders, and form permanent pair bonds. They therefore strike me as less likely to produce hybrids.

The Lost Birds of Paradise is certainly a lavishly illustrated book, reproducing paintings by Gould and other spectacular bird illustrators (some of which I've taken the liberty of re-reproducing), as well as numerous photos and drawings. The distribution and subjects of these illustrations are often a little erratic, however - what's with the naked man in the bath on page 76? - and this same erraticism extends to the text. I can't escape the impression that most of the essays on the various birds were composed separately, with little cross-checking between chapters when the book was compilated. The story of Stresemann's 'overzealous' revisions is repeated a number of times in different chapters, for instance, while many chapters include rather tangential passages on matters related to birds of paradise in general, but not necessarily directly relevant to the specific form the chapter is devoted to (not surprisingly, this is particularly noticeable in some forms known only from single specimens for which otherwise Fuller probably just wouldn't have had that much to say). Probably this eclecticism is most marked in the chapter on 'Paradisaea mixta', in which we are treated to a lengthy quotation from the autobiography of Errol Flynn (complete with full-page photograph) and a description of his experiences trying to start a career collecting birds of paradise in New Guinea some years before he became an actor. And what does this have specifically to do with 'Paradisaea mixta'? As it happens, absolutely nothing.

Still, The Lost Birds of Paradise is easily readable, and at least highlights that the identity of many of the "hybrid" birds of paradise is not as firm as might be thought. A commentor on one discussion thread makes the comment that Fuller obviously really wants there to be overlooked species of birds of paradise, which may lead him to be a bit more hasty in his judgements than he probably should be. Nevertheless, New Guinea, especially the western half, is a surprisingly unexplored place, and as the recent discovery/rediscovery of unknown or near-unknown mammal species there shows, it would be wise to not rule anything out just yet.

The Stately Herons

Taxon of the Week this week may overstep its bounds a little. This is because of a somewhat surprising amount of disagreement about what exactly the taxon in question covers, despite being familiar to people the world around. Prepare to meet the Ardeinae, the herons.

Herons belong to the family Ardeidae, which also includes the bitterns. When I was young and reading Ausich (1961), the division of this family was simple - the bitterns formed the subfamily Botaurinae, while everything else fell into Ardeinae. Since then, however, the picture has become a bit more complicated. The bitterns are almost certainly nested within this broad picture of Ardeinae, and most authors have tended to restrict Ardeinae to birds more closely related to the genus Ardea than to the bitterns. Unfortunately, because different authors have found differing positions for the bitterns within heron phylogeny (McCracken & Sheldon, 1998), this has resulted in differing contents for Ardeinae.

One point that most authors have agreed on is that the family Ardeidae can be divided into four main groups, whatever their inter-relationships might be. These groups are the day-herons (Ardea and its relatives), night-herons, bitterns and tiger-herons. There are also two single-species genera of more uncertain relationships, Cochlearius and Agamia. The South American tiger-herons have been regarded in the past as closely related to the day-herons on the basis of osteological data (Payne & Risley, 1976), but DNA-DNA hybridisation and vocal data position them as the basalmost group in the Ardeidae (McCracken & Sheldon, 1998). Unfortunately, heron phylogeny does not appear to have been given much attention since the DNA-DNA hybridisation days, and the only study I found referred to that used (barely) more advanced molecular methods (Chang et al., 2003) seems to have not included tiger-herons. Payne & Risley (1976) took a conservative approach that referred to each of the four groups as separate subfamilies, while Kushlan & Hancock (2005) included both the night-herons and day-herons in the Ardeinae and placed the other two groups in separate subfamilies. Kushlan & Hancock (2005) also recognised a separate subfamily each for Cochlearius and Agamia, but I suspect this more reflects their uncertain relationships rather than any positive idea about their positions.

The day-herons (Ardeinae proper or tribe Ardeini, depending on whom you ask - Kushlan & Hancock, 2005, divide them into two tribes Ardeini and Egrettini, but that isn't an approach I've seen elsewhere) are the best-known of the groups, and include what most people associate with the name "heron" - long-necked, long-legged, stately birds. The image at the top of this post (from Wikimedia) shows a fairly typical example, the white heron or great egret (Casmerodius albus), while the photo just above (from here) shows the Chinese pond-heron (Ardeola bacchus). As well as the herons of the genus Ardea, this group also includes the egrets (Egretta) and the pond-herons in Ardeola and Butorides. As the common name indicates, the day herons are largely diurnal. The males of a number of day heron species (most notably members of the genus Egretta) produce long decorative plumes in the breeding season, as can be seen in the photo of Casmerodius.

The night herons (Nycticoracini or Nycticoracinae) of the genera Nycticorax and Gorsachius are generally shorter, stouter birds than the day herons, with relatively shorter beaks, as well as (obviously) being nocturnal or crepuscular. Osteological data suggest that the night herons are closely related to the bitterns, while molecular data would place them closer to the day herons (McCracken & Sheldon, 1998). One night heron genus, the American Nyctanassa, is included by Kushlan & Hancock (2005) among the day herons as opposed to with the other Old World night herons.

The boat-billed heron (Cochlearius cochlearius - shown above in an photo stolen from Brian Switek) and the agami heron (Agamia agami - photo below from Arthur Grosset) are both South American oddballs that have been particularly difficult to place among the herons. In the case of Cochlearius, it was regarded as distinct enough that Wetmore placed it in its own separate family. Cochlearius differs from other herons in its unique beak structure and the number of powder-down patches on the chest (four as opposed to three). However, Cracraft (1967) claimed that, except for features directly connected with the beak, Cochlearius was little different osteologically from Nycticorax, and in fact resembled Nycticorax more closely than the other night-heron genus Gorsachius did! While osteological data might indicate that Cochlearius is simply a very specialised night heron, DNA-DNA hybridisation data indicated a more basal position, around the level of the tiger-herons (though unresolved as to which of the two was the basalmost clade - McCracken & Sheldon, 1998). Whichever is the true position, it is clear that the boat-billed heron is highly specialised, though we have little idea what, in fact, it is specialised for - Biderman & Dickerman (1978) found little apparent difference in diet and foraging behaviour of boat-billed herons from more typical heron species, and were only able to suggest somewhat half-heartedly that the oversized beak might be related to courtship displays.

The agami heron (Agamia agami) seems to be a specialist bank feeder (Payne & Risley, 1976). In proportions, it is much like a day heron, and osteological data also associates it with that group. However, if it is a day heron, it differs in a number of characteristics from the other members of that group. As can be seen in the photo above, it is a particularly colourful bird, and it is distinct from the day herons in many features of its adult and juvenile plumage. It also has a particularly slender, needle-like bill. The relationships of Agamia do not seem to have yet been investigated molecularly.


Austin, O. L., Jr. 1961. Birds of the World: A survey of the twenty-seven orders and one hundred and fifty-five families. Paul Hamlyn: London.

Biderman, J. O., & R. W. Dickerman. 1978. Feeding behavior and food habits of the boat-billed heron (Cochlearius cochlearius). Biotropica 10 (1): 33-37.

Chang Q., Zhang B.-W., Jin H., Zhu L.-F. & Zhou K.-Y. 2003. Phylogenetic relationships among 13 species of herons inferred from mitochondrial 12S rRNA gene sequences. Acta Zoologica Sinica 49 (2): 205-210.

Cracraft, J. 1967. On the systematic position of the boat-billed heron. The Auk 84 (4): 529-533.

Kushlan, J. A., & J. Hancock. 2005. Herons. Oxford University Press.

McCracken, K. G., & F. H. Sheldon. 1998. Molecular and osteological heron phylogenies: sources of incongruence. The Auk 115 (1): 127-141.

Payne, R. B., & C. J. Risley. 1976. Systematics and evolutionary relationships among the herons (Ardeidae). Miscellaneous Publications, Museum of Zoology, University of Michigan 150: 1-115.

Linnaeus' Legacy #4

Linnaeus' Legacy #4 is up and running at The Other 95%. This month's keywords: everyone's war against everyone; nine men in the bride's chamber, with one woman; provides suction; every brachyuran; mysteries of the platypus; evil geneticists; Roy Orbison; giganormous rodent; LOLcats; Aetogate.

Giant Cannibal Algae from the Watery Ditch

I didn't think I was going to post anything today - nothing had really grabbed my attention over the last couple of days to write about. But then I look in my e-mail and find a notice about something I really couldn't resist - giant cannibal algae!

Chrysophytes (also known as "golden algae" due to the colour of their chloroplasts) are a class of unicellular algae found in pretty much any aquatic habitat. Your average chrysophyte is not particularly prepossessing - a single cell with one or two flagella emerging from one end and a scattering of chloroplasts within the cell. The image at the top of the post (from here) shows a couple of individuals of one such chrysophyte, Ochromonas. Some chrysophytes produce a covering lorica or coating of scales, while some live in small gelatinous colonies. Chrysophytes can produce resistant statospores or cysts when conditions become unfavourable (in at least some species, this may be induced by increasing population density rather than external environmental conditions), and as a result active populations of chrysophytes often show marked cycles between bloom and quiescent periods. The spore structure of chrysophytes is unique to this group, with a wall composed mostly of silica opening through a collared pore plugged with polysaccharides. Almost all chrysophytes can become heterotrophic (feeding on other organisms) if light conditions are not good enough for photosynthesis, and a number of chrysophytes have ditched chloroplasts altogether and are obligate heterotrophs.

A paper just out today by Yubuki et al. (2008) describes the life cycle of one such colourless chrysophyte, belonging to the genus Spumella. I wasn't able to find a picture of Spumella on the web, but if you imagine Ochromonas without chloroplasts you won't be too far off. Unfortunately, the organisms concerned are not identified to species. This could potentially be a problem as Spumella may be polyphyletically derived from chrysophyte lines that have independently lost chloroplasts (Cavalier-Smith & Chao, 2006). Whatever the species examined actually was, it was recovered from an ephemeral ditch where it would have had to survive periods of drying out.

The single cell that hatched out through the pore of a resistant spore was initially non-motile, but soon sprouted flagella and started to swim. It then produced a gelatinous sphere around itself, which it continued to swim in. The cell then started reproducing by binary cell division at a rapid rate (doubling time at 22°C was about two and a half hours), with the growing cells feeding on bacteria growing within the matrix of the gelatinous sphere, which continued to increase in size as the number of inhabiting cells increased. Eventually, after about two days, the sphere broke down, releasing the swimming cells into the surrounding medium.

Some hours after leaving the sphere, the cells began congregating in swarms of up to forty individuals. It was then that things turned nasty. Some cells within the swarm began capturing others and engulfing them*. Growth of these cannibal cells was rapid, and they soon became two or three times the size of their unfortunate siblings. Finally, the enlarged cannibal cells dropped their flagella and produced their own dormant cysts, waiting for the next stage in the cycle.

*If you can access the original paper, there's an absolutely fantastic sequence of photos of this. You can practically hear the cannibal cell smacking its lips (if it had them) after swallowing its sibling.

Figure from Yubuki et al. (2008), showing the life cycle of Spumella.

The first remarkable thing about this cycle was how quickly it all happened - from initial hatching to re-encystment took only three days. This rapidity is probably an adaptation to the unstable habitat that the organism lives in - reproduction and encystment has to be complete by the time the water supply dries up. The gelatinous matrix inhabited by the growing cells seems to facilitate this rapid life cycle by encouraging the growth of bacteria and providing the cells with a ready food supply (offhand, such a gelatinous matrix in which the cells are free-swimming has previously been described from only a single other organism - another chrysophyte, Chromulina nebulosa). The cannibalism within the swarm may also serve the same purpose. Cannibalism has been recorded in other protist species, but seems in those cases to be an opportunistic response to disappearing food supplies. In Spumella, cannibalism may be obligate - when individuals of two other protist species, Bodo and Ochromonas, both comparable in size to the cannibalised Spumella, were added to the medium, they were completely ignored and the cannibal Spumella continued to feed only on members of their own species.



Cavalier-Smith, T., & E. E.-Y. Chao. 2006. Phylogeny and megasystematics of phagotrophic heterokonts (kingdom Chromista). Journal of Molecular Evolution 62 (4): 388-420.

Yubuki, N., T. Nakayama, & I. Inouye. 2008. A unique life cycle and perennation in a colorless chrysophyte Spumella sp. Journal of Phycology 44 (1): 164-172.

Tangled Bank

The Tangled Bank is a fortnightly carnival that highlights the best in science and medicine blogging. This week's edition is up at Quintessence of Dust.

Also, a reminder that Linnaeus' Legacy is scheduled to happen at The Other 95% tomorrow. If you've got any last minute submissions, get in quick!

Sculpins Go Wild

Yokoyama, A., & A. Goto. 2005. Evolutionary history of freshwater sculpins, genus Cottus (Teleostei; Cottidae) and related taxa, as inferred from mitochondrial DNA phylogeny. Molecular Phylogenetics and Evolution 36 (3): 654-668.

Freshwater sculpins of the genus Cottus are a widespread Holarctic group of smallish fishes, belonging to the suborder Cottoidei (the image at top, from Wikimedia, shows Cottus gobio). While most members of the Cottoidei are marine, there are a number of freshwater taxa - about 40 species in Cottus, three in Myoxocephalus (a genus also including marine species), the monotypic genera Mesocottus and Trachidermus, and 33 species divided between three families and 12 genera found in Lake Baikal in central Siberia. Species of Cottus show a wide diversity of life histories, from catadromous (species that live in fresh water before travelling to the sea to spawn) to amphidromous (species that can move between fresh and salt water, but don't do so specifically to spawn - the amphidromous Cottus species are freshwater spawners) to species that are permanently freshwater. As such, Yokoyama and Goto (2005) investigated the phylogeny of this genus using the mitochondrial 12S rRNA and CR (control region) genes to discover its biogeographical history and how the different life histories have evolved.

Previously, the catadromous life cycle has been thought to be ancestral for Cottus, both because freshwater cottoids as a whole are certainly derived from marine ancestors, and because the catadromous Trachidermus fasciatus was identified on morphological groups as the sister group to Cottus. The amphidromous lifestyle was thought to have arisen next, from which increasing specialisation for freshwater habitats had given rise to the purely fluvial (river) or lacustrine (lake) species. The results of Yokoyama and Goto did not contradict the basal position of catadromy, but added a twist - the single catadromous species, Cottus kazika, did not group with the remaining Cottus species, but instead was sister (with high support) to Trachidermus fasciatus, making Cottus polyphyletic (Shedko & Miroshnichenko (2007) have since moved C. kazika out of Cottus as a result, resurrecting an old genus name to label it Rheopresbe kazika). The role of catadromy in the evolution of Cottus therefore becomes a bit more uncertain.

The remaining, freshwater-spawning species of Cottus were supported as a clade, admittedly with low support though the shared life history makes the clade credible. As for whether the amphidromous life style was indeed ancestral to the purely freshwater, Yokoyama and Goto's results seemed to suggest the exact opposite, with the amphidromous species scattered through the various clades of purely freshwater species, and not particular basal within those clades. However, the authors themselves were a little more agnostic about their results - they point out that repeated parallel loss of amphidromy could give a falsely parsimonious appearance of derived amphidromy. Biogeography-wise, their results supported the traditional view of an origin of Cottus somewhere in eastern Eurasia, where the greatest diversity of species is found. Four reasonably well-supported clades of freshwater-spawning species were identified - two restricted to eastern Eurasia and Japan, one found across Eurasia, and one (their clade E) including both Eurasian and North American species.

The non-monophyly of Cottus goes further than just one wayward species, though. You recall that I mentioned the diverse fauna of freshwater cottoids endemic to Lake Baikal? In the past, species of this fauna were divided between three families - some in Cottidae with the other freshwater sculpins, some in an endemic family Abyssocottidae, and a separate family for the unique genus Comephorus. However, molecular analysis (Kontula et al., 2003) had discovered that the Baikal cottoids formed a single clade, and had probably originated from a single colonisation of the lake by an ancestral species. Once in the lake, the cottoids had diversified rapidly (molecular clock calculations, for what they're worth*, estimate an age of 1.2 to 6.2 million years for the Baikal radiation) to occupy a number of niches, including some not occupied by sculpins anywhere else in the world. The pictures above give some indication of the diversity of Baikalian cottoids - the pelagic Cottocomephorus inermis (from here) on the right, an unidentified benthic species reasonably similar to a typical cottid (from here) in the centre, and the highly derived pelagic Comephorus on the left (image from here).

*Okay, so I don't trust molecular clocks as far as I can throw them or the researchers who calculate them. In this case, unfortunately, they're all the evidence we have.

The point where it all becomes really interesting, though, is that not only does this diversity derive from a single point, but it is actually nested within the genus Cottus! This had previously been suggested by Kontula et al. (2003), and so Yokoyama & Goto (2005) took the opportunity to test Kontula et al.'s results against their more extensive dataset by including the data from the earlier study. While support was not impressive, the Baikalian radiation seems to be nested within Yokoyama & Goto's clade E.

As usual, though, I did come away from this paper with a few questions. Yokoyama and Goto used only one marine species and a member of Myoxocephalus as outgroups, and while they did find the Trachidermus + Rheopresbe clade as sister to the freshwater-spawning clade, support was very low and the position was not statistically supported. Is there actually a direct connection between these two clades, or did the catadromous species gain their freshwater lifestyle independently from the freshwater species? Answering this question will be vital to understanding what (if any) role catadromy may have played in the transition of the ancestors of Cottus from marine to freshwater habitats. And what of the untested freshwater Mesocottus haitej? Does this Siberian species represent another independent movement into freshwater, or does the paraphyly of Cottus extend even further?


Kontula, T., S. V. Kirilchik & R. Väinölä. 2003. Endemic diversification of the monophyletic cottoid fish species flock in Lake Baikal explored with mtDNA sequencing. Molecular Phylogenetics and Evolution 27 (1): 143-155.

Shedko, S. V., & I. L. Miroshnichenko. 2007. Phylogenetic relationships of sculpin Cottus volki Taranetz, 1933 (Scorpaeniformes, Cottidae) according to the results of analysis of control region in mitochondrial DNA. Voprosy Ikhtiologii 47 (1): 27-30 (transl. Journal of Ichthyology 47 (1): 21-25).

Taxon of the Week: Nothing to do with Teapots

This piece of rudeness was more than Alice could bear: she got up in great disgust, and walked off; the Dormouse fell asleep instantly, and neither of the others took the least notice of her going, though she looked back once or twice, half hoping that they would call after her: the last time she saw them, they were trying to put the Dormouse into the teapot.
--Lewis Carroll, Alice's Adventures in Wonderland

The dormouse was an animal that I had heard of long before I knew what one actually was, solely as a result of its appearance in Alice's Adventures in Wonderland, a book I read countless times as a young'un (the image at the top, a reproduction of one of John Tenniel's original illustrations for Alice, comes from here). Those of you who have read the book will recall that the main characteristic of the Dormouse was its continually falling asleep - doubtless because, Alice's Adventures being set in July, it was time the dormouse should have been hibernating.

Okay, the picture's obviously posed (if not photoshopped) using a hibernating dormouse, but sometimes cuteness is irresistable and I thought it might draw a larger audience among Japanese schoolgirls (image from the Cellar). Dormice (Gliridae*) are a smallish family of mostly Palaearctic rodents. The name is supposed to come from the same source as the word "dormant" and refers to the hibernation by species in colder climates. Dormice do resemble rather solidly built mice, but features of the internal anatomy, supported by molecular data, indicate that Gliridae are not, in fact, close relatives of the Muroidea (mice and rats proper) but are more closely related to the Sciuroidea (squirrels), their mouse-like features having arisen convergently (Maier et al., 2002). The relatively long fossil record of Gliridae, dating back to the Eocene, also supports a more basal position for the family.

*Some references will use the name Myoxidae for the same family. There may also be a single family Gliridae, or a superfamily Gliroidea containing two families, depending on whether the specialised Selevinia (see below) is regarded as belonging to a separate family or as a derived member of the Gliridae.

Dormice are seemingly fairly omnivorous. Animal Diversity Web describes their diet as "feeding on fruit and nuts and also eating invertebrates, birds and their eggs, and sometimes other rodents". One rather unique species, the rare Selevinia betpakdalensis of Lake Balkhash in Kazakhstan (shown in an illustration from Animal Diversity Web above), has a highly reduced dentition (see image below from here) and is mostly insectivorous.

The tendency of hibernating species to stack on the fat in preparation for winter gives rise to the common name of the European species Glis glis - the edible dormouse. This species was eaten in Imperial Rome, though the image below (from The Daily Mail) suggests that it may have been a little difficult to get the apple into its mouth. The Old Foodie has a recipe for stuffed dormouse taken from a translation of Apicius*, while Roman History Books and More also gives a quote from Petronius referring to dormice coated with poppy seeds and honey. Tasty!

*I'm a little confused about the "laser" that is supposed included in the stuffing. Is this a misprint for "laver" (an edible seaweed), or is there actually a vegetable by that name?


Maier, W., P. Klingler & I. Ruf. 2002. Ontogeny of the medial masseter muscle, pseudo-myomorphy, and the systematic position of the Gliridae (Rodentia, Mammalia). Journal of Mammalian Evolution 9 (4): 253-269.