Perciformes Go Bye-Bye?

Anableps anableps, the four-eyed fish, a member of the newly-named clade Stiassnyiformes. The upper and lower halves of the eyes have different focal distances, allowing the fish to see clearly both above and below the water. Photo from here

Not so long ago, I referred to the unholy taxonomic mess that besets the Acanthomorpha (spiny-finned fishes), the clade that includes (among others) the majority of familiar marine fish, with a large number of acanthomorphs previously dumped in a cluster called "Perciformes". "Perciformes", I'll remind you, was ichthyological code for "morphologically somewhat boring fish that aren't distinctive enough to be called anything else".

Just yesterday, I received notification of a new paper (Li et al., 2009) that identifies a number of the same clades recovered in papers such as Dettai & Lecointre (2005) (which is not entirely surprising because both Dettai and Lecointre are also authors on this one). Where Li et al. (2009) differs from previous studies, however, is that it actually introduces a whole bunch of new names for the clades it finds. (Sadly, they also do something that is a bit of a pet peeve of mine, what I call "stealth taxonomy" - introducing new taxa in a paper without indicating that they're doing so in the title or mentioning their names in the abstract).




The above diagrams from Li et al. (2009) represent a supertree for the Acanthomorpha taken from the results of Li et al.'s analyses. It's been broken into four parts because that's a lot of fish. You may need to click on the images to get a higher resolution picture to follow the next bit.

The clade labelled P at the bottom of the tree doesn't get a name - some studies have found it as monophyletic, some haven't. What does get a name is the clade A uniting the Zeiformes (dories) and Gadiformes (cods) - Zeioigadiformes. That, my friends, is not a name to attempt whilst drunk. The Beryciformes (squirrelfishes and allies) are paraphyletic in the supertree (they're the first three clades leading towards the big P' clade), but some studies (including one of the analyses of Li et al. themselves) still find it to be monophyletic - another watch this space moment. The Ophidiiformes (cusk-eels, etc. - including the Carapidae that are famed for living inside the recta of sea cucumbers) are sister to the P' clade, which is what recent studies have come to call Percomorpha. Batrachoidiformes (toadfishes) are sister to the remaining percomorphs, but as you can see there's still a lot of messiness otherwise. Still, there are a few big clades that can be recognised, most notably the Q, L and X clades.


Sphyraena barracuda, now a member of the Carangimorpha. Photo from here.

The Q clade includes the Atherinomorpha, Mugilidae (mullets), Blennioidei (blennies) and, in most studies, the Cichlidae (cichlids), though in the supertree the cichlids are apparently feeling a bit stand-offish. Li et al. dub this clade the Stiassnyiformes, for reasons sadly unexplained. The L clade, which Li et al. dub the Carangimorpha, includes the big pelagic fish such as dolphins, trevally, marlins, tuna and mackerel, as well as the flatfish. Within the L clade, things are still rather messy, but this is mainly the fault of the flatfish still trying to make themselves look polyphyletic despite all morphological reason.


Unidentified icefish (Notothenioidei). Photo by Uwe Kils.

The X clade is labelled by Li et al. the Serraniformes. I'm guessing that they decided, probably wisely, that "Perciformes" carries just a little to much baggage. Notable members of this clade include the Percidae, Notothenioidei (Antarctic icefishes), Gasterosteidae (sticklebacks) and what were the Scorpaeniformes (now known to be polyphyletic).


Indostomus paradoxus, the armoured stickleback or paradox fish of south-east Asia. Photo from hwchoy.

A couple of smaller clades that rate a mention are the F and G clades. The F clade (now the Anabantiformes) includes the Anabantoidei (gouramis), Channidae (snakeheads), Indostomus (the paradox fish) and Synbranchiformes (swamp eels). The association of these taxa forms an intriguing clade of Old World tropical freshwater fish, with their diversity centred around southern Asia. The G clade includes an assortment of "trachinoid" fishes such as stargazers and torrent fish, but not the Trachinidae themselves. Fittingly, Li et al. label this group the Paratrachinoidei.

Part of the problem with dropping the idea of "Perciformes", to date, has been that to do so would leave a massive pile of unplaced families just flopping all over the place. Hopefully, with the pile of new clade names presented to us by Li et al., a big step has been taken towards allowing us to never have to say "Perciformes" again.

REFERENCES

Dettai, A., & G. Lecointre. 2005. Further support for the clades obtained by multiple molecular phylogenies in the acanthomorph bush. Comptes Rendus Biologies 328 (7): 674-689.

Li, B. A. Dettaï, C. Cruaud, A. Couloux, M. Desoutter-Meniger & G. Lecointre. 2009. RNF213, a new nuclear marker for acanthomorph phylogeny. Molecular Phylogenetics and Evolution 50: 345-363.

Musical Interlude - Eartha Kitt, 1927 - 2008

Every gay man is supposed to have his diva, and the woman whom I would have claimed as mine, I've just learnt, passed away this last Christmas Eve. The girl who once told us that, "If I can't take it with me when I go, I just ain't gonna go" has, well, gone, with timing that can only be applauded for its irony in light of what was, perhaps, her most famous production:



Though favourite tracks of mine include "Monotonous" ("For thirty days, salt air I sniffed, while I was being cast adrift with a man who looked like Montgomery Clift - monotonous"), "Usku Dara", "Old-Fashioned Girl" ("I like the old-fashioned flowers - violets are for me. Have them made in diamonds by the man from Tiffany's), "Sous les Ponts de Paris" and this:



Goodbye, Eartha, and thank you.

Thought-Crime: I Have Slandered the Gelatinous

The video at the end of this post comes via Miriam Goldstein. The beasty (or, technically speaking, colony of beasties) that it shows is a siphonophore not unlike the Physophora hydrostatica illustrated by Haeckel near the beginning of the 1900s:



Siphonophores were covered here back in August, and that post will (hopefully) help you understand just what you're looking at here. Nevertheless, the video above still stunned me. I had assumed that Haeckel had been employing a certain amount of (not entirely uncharacteristic) artistic licence in drawing those curly palpons (the fat tentacle-like structures) - the still photos of siphonophores I had seem looked as if they would be fairly stiff in real life. How wrong I was! Watch the video - those things are sinuous.



Need I remind you that siphonophores can be up to 30 m in length, and severely toxic? Pleasant dreams, kiddies.

2008 Retrospectus

It is now officially 2009 - or at least I assume it is. These days, I'm old and grizzly enough that I no longer feel the compulsion to stay up late on December 31st to make sure the clock ticks over to 12:01 like it should do. Still, a look back at the year here at Catalogue of Organisms might not go amiss.

Over the course of 2008, yours truly has put up 201 posts, meaning an average of one post every 1.82 days. I tell you, it's times like this that make me think - I'm really not doing enough work on my thesis. Not that I've been entirely unproductive on that front - two short papers have been published:

Taylor, C. K. 2008. A new species of Monoscutinae (Arachnida, Opiliones, Monoscutidae) from New Zealand, with a redescription of Monoscutum titirangiense. Journal of Arachnology 36: 176-179.

Taylor, C. 2008. A new species of Monoscutidae (Arachnida, Opiliones) from the wheatbelt of Western Australia. Records of the Western Australian Museum 24. (No page numbers for that one because it's only come out from the press within the last few days, and I haven't received a copy myself yet.)

The first of these established the new genus and species Templar incongruens (Templar because it's heavily armoured and the female has a cross-shaped marking on its back), and the second presents Megalopsalis linnaei (named in commemoration of Linnaeus' 300th birthday, and part of a special commemorative issue of the Records containing a number of new species so-named - I don't know what the rest are yet, though I do know that there's a scorpion in there).

There's another manuscript which is very close to completing review (I'm just making the last few requested edits) and two which are completed but awaiting submission. A couple of those will definitely be featuring here once they're published, so watch this space.

The Catalogue averaged 138 visits per day for 2008. The busiest day was the 29th of August, when 403 people passed by. Over half of those were sparked by Larry Moran linking to a post of mine on Gould and Lewontin's Spandrels paper. For the record, I'm not entirely happy with that post myself - I think it ended up sounding too positive about its subject. But that's the problem with the Spandrels paper - like the Bible and the Origin of Species, its social significance has become something above and beyond its actual content (which, in the case of Spandrels, is actually kind of weak). Larry was also responsible for the popularity of the most-visited post of the year, on the origin of flowering plants. Larry has linked to me a few times over the year, and every time has caused a big spike in my readership, so I would like to extend my formal thanks to him at this point.

My personal favourite posts of the year include the angiosperm origins post I've just linked to, as well as posts on why ceratopsids aren't worth it and baleen whales. The report of an articulated fossil of a machaeridian had the paper's first author putting an appearance in the comments, and inspired me to devote an entire week to scleritome fossils that was some of the most fun I had on this site this year. I also got first-author attention for the Sophophora melanogaster post (still waiting for a decision there, in case you were wondering). I was rapturous over my first ever observations of entoprocts and tardigrades, though sadly I never did successfully isolate those follicle mites.

I've been quite proud of some of the posts I've written on taxonomic principles. Hopefully, my post on the use of Latin in biological names has been useful to some people. The closure of the Utrecht Herbarium lead me to write some hopefully worthwhile posts on the importance of type and voucher specimens. The latter was followed by a right royal whinge about how few studies bother depositing voucher specimens. The Aetogate debacle led to a post on publication ethics that had (gosh) Kevin Padian commenting with (needless to say) greater clarity and effect than the post itself. And the accidental release ahead of time of the draft for what was to become Epidexipteryx lead to my speaking on the role of electronic publication in taxonomy, followed only a few weeks later by the release of the ICZN proposals on just that matter.

I've also written on some of the year's most fascinating publications - the aforementioned machaeridian (still my nomination for the greatest announcement of 2008), cannibalism in the life-cycle of a heterotrophic alga, the experimental induction of the next phase in the unknown life-cycle of y-larvae, a photosynthetic relation for Sporozoa, the Waptia chain, and within the last two days, the Attercopus redescription.

So all in all, I hope not time completely wasted. 2009 promises (or "threatens" might be more appropriate) to be an eventful year - I have to finish my thesis this year (argh!) and then try to actually find employment (oh dear). To quote Patrick McGoohan - "Be seeing you".

Carnivalia

Berry Go Round #12 is up at Foothills Fancies.

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

Attercop

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

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

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

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

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



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


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

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


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

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

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

REFERENCES

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

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

Streps

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

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

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

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

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

REFERENCES

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