Field of Science
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From Valley Forge to the Lab: Parallels between Washington's Maneuvers and Drug Development4 weeks ago in The Curious Wavefunction
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Political pollsters are pretending they know what's happening. They don't.4 weeks ago in Genomics, Medicine, and Pseudoscience
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Course Corrections5 months ago in Angry by Choice
Happy Birthday to Me (with Random Videos)
Well, not to me, per se, but today it has been two years since Catalogue of Organisms was launched on the intertubes. I'm not sure what exactly two translates to in blog years, but it's certainly old enough to not get asked for ID when it goes to the pub. So, just like last year, here's the summary of the Catalogue's most popular posts:
No. 10 - Bird Phylogeny: Though personally I'd say forget this one, read the much more detailed review of the same paper by Nicholas Sly (just ignore the bit in the comments where Nick and I - particularly I - manage to embaress ourselves about Himantornis). I should also mention No. 11, the Drosophila post, because No. 10 is currently leading No. 11 by only a single page-view.
No. 9 - Most Unbelievable Organisms Evah!: Maybe not one of my most rigorous posts, but it certainly was fun to write. Go, read about Acarophenax reproduction - just try not to think about it too much.
No. 8 - Thalassocnus: No, this was not a joke. The marine sloth really did exist.
No. 7 - Sex Determination in Leiopelma: (Nearly wrote Leiolopisma there. I always get those two mixed up.) I love the idea of a genus that has more methods of sex determination than recognised species.
No. 6 - The Species-Scape: Though as this was a short post built around someone else's image, I can't claim any credit for it. Still a cool concept, though.
No. 5 - Aquificae: The popularity of this post can be mostly attributed to one factor - it's cited as a source on Wikipedia. That, and of course the fact that bacteria rock.
No. 4 - The Origin of Angiosperms: Take note that this post was inspired entirely by a particularly cretinous comment that had been made in response to No. 10.
No. 3 - Daddy Long-legs: I still hate that name.
No. 2 - Gulper Eels: Last year's champion post has been knocked off its perch. One point I still don't understand - what the heck is the deal with snipe eel jaws? What on earth is the use of jaws you can't even close properly?
And the most popular post of the last two years:
No. 1 - Boobies: Despite only being posted a few months ago, the popularity of this post has been astounding. "Boobies" seems to have almost beaten out "frog sex" for the title of Google Search Most Commonly Bringing People to this Site. Beats me - I guess some people just really like boobies.
Oh Crake (Taxon of the Week: Amaurornis)
The Rallidae are undeniably a very successful group of birds. Rallids have spread to almost every corner of the globe, including a few island corners that were never reached by other terrestrial birds. The subject of today's post is one of the widespread genera of rallids - but it's one of the trickier ones.
Stable classification of rallids has eluded ornithologists for years, for two main reasons. One is that rallids are a prime example of what may be called the smudge effect - clearly distinct subgroups, but without clear boundaries. Take a rail and a moorhen, and the differences are easy to spot. But then someone comes along with a third species, that looks a bit like a rail and a bit like a moorhen, and it's back to the bench for the frustrated ornithologist. The other is the unusual nature of rallid evolution and dispersal. Rallids are, normally, surprisingly good fliers - that's why they are able to reach so many remote islands. On the other hand, they tend to be very reluctant fliers, only invoking those flying abilities if they absolutely have to. As a result, rallids have tended to disperse to remote localities, and then promptly lost the flying abilities that got them there at the first available opportunity. With those losses of flying ability come other related changes - larger body size and such - resulting in the flightless rails looking not very much like their flying descendants, and an awful lot like unrelated flightless species from completely different islands.
The genus Amaurornis belongs to the subgroup of rallids known as the crakes. Crakes are quite generalised rallids, distinguished from the other major generalised rallid group, the rails, by their shorter beaks. Most crakes are notoriously shy and retiring birds - as an example of their reserve, one crake species, Amaurornis magnirostris of the Talaud Islands in Indonesia, was only described in 1998 (Lambert, 1998). The crake species assigned to Amaurornis, also known as bush hens or water hens, tend to be larger than other crake species in the genus Porzana and its satellite genera. Other than this, however, there seems to have been little or no definition on what actually distinguishes one genus from the other, and species have been shuttled back and forth between the two for years.
Indeed, Olson (1973) regarded Amaurornis as the generalised ancestral group for a number of other rallid genera, including Porzana, Porphyrio (swamphens), Gallinula (moorhens) and Fulica (coots) - effectively paraphyletic, except that he didn't suggest any specific relationships between descendant genera and particular species within Amaurornis. As well as the Asian and Australasian species previously included in the genus, Olson (1973) also assigned three African species previously regarded as the genus Limnocorax to Amaurornis.
The first explicitly phylogenetic analysis of the Rallidae (and still the only morphological analysis of the group) was the gigantic production of Livezey (1998). Livezey confirmed Olsen's suggestion of a close relationship between Amaurornis, Porzana, Gallinula and Fulica (but not Porphyrio), but Porzana was massively paraphyletic, with the other three genera belonging to a clade that was nested within Porzana - specifically within the subgenus Limnocorax (which Livezey had removed from Amaurornis and returned to Porzana so that at least one of the genera could be monophyletic). Livezey refrained from carving up Porzana into bite-sized monophyletic chunks because support for the recovered relationships within the genus was negligible, and while he did support monophyly for the core group of Amaurornis, it apparently didn't take much fiddling with the analysis to make the whole thing topple over like a badly-cooked soufflé (certainly, Livezey's taxonomic separation of Amaurornis from the other crakes as a separate subtribe Amaurornithina fits right into the "tits on a bull" category). There are also hints that convergence may have befuddled a number of results of the Livezey analysis - elsewhere in the tree, for instance, was a highly suspect clustering of flightless taxa from New Zealand and Mauritius.
Subsequent molecular analyses have tackled sections of the Rallidae, but unfortunately none have had the coverage of the Livezey (1998) analysis. The most significant for the crakes has been that of Slikas et al. (2002), which answered the hanging question of "is Porzana or Amaurornis the polyphyletic genus?" with "As it happens, they both are". Their analysis divided Porzana and Amaurornis between three clades - one containing species of the former, one containing species of the latter, and one containing species of both. Christidis & Boles (2008) proposed that the names Porzana and Amaurornis be each restricted to the appropriate one of the first two clades, with the third clade recognised as a third genus. Oh, and the correct name for that third genus just happens to be Limnocorax. That's right - after years of being the subject of a game of taxonomic kickball, Limnocorax breaks free to become its own genus - and one considerably larger than either of the other two. Unfortunately, Slikas et al. didn't include any representatives of Gallinula or Fulica to test where they sat relative to the three clades.
If we accept the results of Slikas et al. (2002), Amaurornis includes five species from southern and south-east Asia and northern Australasia - A. olivacea, A. isabellina, A. phoenicurus, A. moluccana and A. magnirostris*. Most of these are some variation on chestnut-brown, but the striking white-breasted A. phoenicurus is a notable exception. An unfortunate omission from Slikas et al.'s (2002) analysis was the large New Guinean flightless rail Megacrex inepta, which was placed in Amaurornis by Livezey (1998). A molecular analysis by Trewick (1997) that included Megacrex placed it in association with Rallus and its relatives (the rails), and far away from Porzana, but (a) none of the other "Amaurornis" species were included in this analysis, and (b) it was a neighbour-joining analysis. Yuck.
*Brief taxonomic note - Amaurornis is one of those genera that has been subject to argument about whether it is masculine or feminine. It's feminine, so the species names have to be formed accordingly (phoenicurus retains the masculine ending because it's a noun, not an adjective).
REFERENCES
Christidis, L., & W. Boles. 2008. Systematics and Taxonomy of Australian Birds. CSIRO Publishing.
Lambert, F. R. 1998. A new species of Amaurornis from the Talaud Islands,
Indonesia, and a review of taxonomy of bush hens occurring from the
Philippines to Australasia. Bulletin of the British Ornithologist’s Club 118 (2): 67 – 82.
Livezey, B. C. 1998. A phylogenetic analysis of the Gruiformes (Aves) based on morphological characters, with an emphasis on the rails (Rallidae). Philosophical Transactions of the Royal Society of London Series B – Biological Sciences 353: 2077-2151.
Olson, S. L. 1973. A classification of the Rallidae. Wilson Bulletin 85 (4): 381-416.
Slikas, B., S. L. Olson & R. C. Fleischer. 2002. Rapid, independent evolution of flightlessness in four species of Pacific Island rails (Rallidae): an analysis based on mitochondrial sequence data. Journal of Avian Biology 33: 5-14.
Trewick, S. A. 1997. Flightlessness and phylogeny amongst endemic rails (Aves: Rallidae) of the New Zealand region. Philosophical Transactions of the Royal Society of London Series B – Biological Sciences 352: 429-446.
My Genitals Just Grew Eyes and Swam Away: The Life of a Syllid Worm
It is currently Sex Week at Deep-Sea News, and this post is written in honour of that event. Sex, after all, is a big part of biology (hur, hur, hurr).
Marine worms of the family Syllidae are small polychaetes, usually less than two centimetres in length and about a millimetre in width. Many syllids are interstitial (living buried in sand), others live in association with corals or sponges (on which they may feed). The main feature of syllids that has captured people's attention, however, is their extremely multifarious sex lives (Franke, 1999).
Syllids are one of a number of polychaete families exhibiting what is called epitoky, a significant metamorphosis between the juvenile or atokous and sexually mature or epitokous stages. The originally benthic worm grows long, extended parapodia, and the eyes and other sensory organs become greatly enlarged. More significantly, the reproductive tissue expands to fill almost the entire body, and other organs such as the digestive system degenerate, so the final epitokous worm is basically a highly sensitive pelagic gonad. In other worms such as members of the family Nereididae, the mature worm will swim up into the water column to meet up with other pelagic gonads, after which the entire mass will explode in a cloud of gametes.
Syllids, however, do things a little differently. Seemingly not as keen on ending life with a bang, they have evolved a number of ways to continue on with their life after maturity. The original syllid mode of reproduction involved metamorphosis to an epitoke as in other related polychaete families, but without the degeneration of the digestive system. And nereidids release their gametes by fatally rupturing the body wall, syllid epitokes release theirs through modified nephridia. Afterwards, the syllid epitoke is able to return to the ocean floor and partially revert back to its original atokous form, ready to reproduce another year. This mode of reproduction, called epigamy, remains the one used in two of the four syllid subfamilies, Eusyllinae and Exogoninae, as well as part of the subfamily Autolytinae.
Two other syllid lineages, the remainder of Autolytinae and the subfamily Syllinae, developed a mode of reproduction called schizogamy - the joy of budding. In schizogamous syllids, instead of the whole worm developing into an epitoke, a separate epitoke buds off the original atoke. In the most basic form of schizogamy, it is the posterior part of the worm that metamorphoses into the epitoke, in most cases growing its own separate, fully-developed head before breaking away from the anterior "parent" part (some Syllinae have headless epitokes). In some syllids, another epitoke may begin developing in front of the original epitoke before it breaks away, and possibly even more, so that the animal turns into a chain of developing worms. Others produce a number of epitokes growing in a bunch. After the epitoke(s) break off, the remaining atoke will regenerate any losses. Indeed, the atoke may begin regenerating even before the epitoke breaks off - the left and right sides of the new posterior part grow on either side of the epitoke, and once the epitoke is gone they fuse together down the middle.
Very few syllids have developed true asexual reproduction, where they fragment to give rise to new atokes instead of epitokes. But no survey of syllid budding would be complete without mention of the most bizarre of all syllids, the deep-sea sponge-dwelling Syllis ramosa. In this species (shown above in a drawing from here), buds develop laterally but don't detach from the parent worm. As these lateral buds grow, they start growing their own lateral buds, so that over time the worm develops into a branched network, spreading through the channels of its hexactinellid host.
REFERENCES
Franke, H.-D. 1999. Reproduction of the Syllidae (Annelida: Polychaeta). Hydrobiologia 402: 39-55.
Who Left All this Fish Lying Around (Taxon of the Week: Neopterygii)
The Neopterygii, or "new fins" (not, as it is often translated, "new wings") are one of the most successful clades of fishes today. One particular subgroup of the Neopterygii, the teleosts, includes almost all the living ray-finned fishes. However, just to be difficult, I decided that the most appropriate tack for a post on Neopterygii was to leave the teleosts in all their diversity for another time, and focus on the non-teleost neopterygians. This, as it turns out, was a mistake. The non-teleost neopterygians seem, to a fish, to be almost universally ignored, and most of what there is out there was covered by Toby White almost seven years ago. Nevertheless, I'll see what I can do.
The origins of the Neopterygii date back to sometime in the Permian (Hurley et al., 2007). Compared to earlier actinopterygians, the ancestors of Neopterygii lost their clavicle, beginning a trend of lightening and strengthening their skeletons, while at the same time reducing the weight of their scales. Early fish had been heavily armoured arrangements, but like the origins of the modern military, neopterygians were to trade in their clunky plate armour for something a bit more like a bullet-proof jacket*.
*Something that has almost nothing to do with the main post, but which struck me when I was thinking about it yesterday evening: When one looks at the living vertebrates only, it is easy to imagine that there was a progressive development of the bony skeleton - at the base of the tree, we have the living cartilaginous fishes and jawless fishes with little or no ossification, followed by the bony fishes and the tetrapods mostly with full skeletons. The fossil record, however, indicates that things were a little more complicated - early fishes such as placoderms had extensive skeletons, and the modern unossified fishes are actually the descendants of vertebrates that lost most of their skeletons. However, the original vertebrate bony skeleton did differ from the modern bony skeleton in one major regard - it was on the outside. Early fish had great coverings of bony armour, but little ossified interior skeleton. So over the course of evolution, vertebrates have gone from having their skeletons on the outside and meaty parts in the middle, to have the meaty parts on the outside and the skeletons in the middle. In other words, vertebrates have effectively been turned inside out.
There are few living groups of non-teleost neopterygians - in fact, there's only two, both restricted to fresh waters of North America. One group, the Halecostomi, is represented in the modern fauna by only a single species, the bowfin, Amia calva. As Toby has noted before me, perhaps the single most remarkable feature of the bowfin is that it has absolutely nothing remarkable about it whatsoever. Amiid fishes go all the way back to the Jurassic, and don't look too much different from each other in all that time. The other living group, the American gars of the family Lepisosteidae, are entirely a different matter - gigantic carnivorous fish, with long beaks and sharp teeth. The largest gars can be over two metres long, and according to this site Rafinesque referred to gars up to twelve feet long. They also lay eggs that are toxic to humans. Unfortunately, it looks like American gars don't have green bones, despite common rumour - the green-boned "garfish" is a quite different, marine fish (Belone) nestled well within the teleosts.
Relationships between the neopterygian clades are almost completely obscure - while features of the jaw musculature support a relationship between Amia and teleosts to the exclusion of gars, other authors have supported an Amia-Lepisosteidae clade that excludes teleosts. Hurley et al. (2007) found the latter result in a morphological analysis, but the former in a molecular analysis. While a number of fossil groups of non-teleost neopterygians are known, few authors seem to have plugged them into a phylogenetic analysis except for Hurley et al. (2007) and Arratia (2001) (the latter of which I don't have access to). A number of authors have supported a relationship between the gars and the extinct Semionotiformes (Olsen & McCune, 1991), while the Pachycormiformes and Aspidorhynchiformes seem likely to be stem-teleosts. Finally, the Dapediidae and Pycnodontiformes were found by Hurley et al. (2007) to form a third clade in a polytomy with the Amia-Lepisosteidae clade and the teleosts.
Some of these were decidedly odd fishes. The Pycnodontiformes were deep-bodied fish, about as tall as they were long. They had strong teeth, and would have fed on shellfish. The Pachycormiformes, mostly pelagic hunters, are best known through the monster Leedsichthys, a gigantic filter feeder growing to lengths over ten metres, which is probably the largest known ray-finned fish.
Perhaps the coolest of all, though, were the Semionotidae. Semionotus wasn't anything much to look at - not spectacularly large (probably about half a foot) and pretty generalised morphologically. During the Mesozoic it was found in freshwater deposits pretty much around the world, so it would have been dirt common. Where things get interesting is when you get to the Late Triassic and Early Jurassic Newark Supergroup of eastern North America. The Newark Supergroup comprises a series of lake deposits, formed by a process of rifting similar to the modern Great Lakes of Africa. And Semionotus was the Newark deposits' cichlid. Within a single lake deposit, a whole series of Semionotus species can be found, varying from long and narrow to deep-bodied and humpbacked (McCune, 2004). And that is very cool - that the incredible African cichlid radiation is not so incredible after all, but represents patterns and processes that were just as active 100 million years ago.
REFERENCES
Arratia, G. 2001. The sister group of Teleostei: consensus and disagreements. Journal of Vertebrate Paleontology 21 (4): 767-773.
Hurley, I. A., R. Lockridge Mueller, K. A. Dunn, E. J. Schmidt, M. Friedman, R. K. Ho, V. E. Prince, Z. Yang, M. G. Thomas & M. I. Coates. 2007. A new time-scale for ray-finned fish evolution. Proceedings of the Royal Society of London Series B 274: 489-498.
McCune, A. R. 2004. Diversity and speciation of semionotid fishes in Mesozoic rift lakes. In Adaptive Speciation (U. Dieckmann, M. Doebeli, J. A. J. Metz & D. Tautz, eds) pp. 362–379. Cambridge University Press.
Olsen, P. E., & A. R. McCune. 1991. Morphology of the Semionotus elegans species group from the Early Jurassic part of the Newark Supergroup of eastern North America with comments on the family Semionotidae (Neopterygii). Journal of Vertebrate Paleontology 11 (3): 269-292.
All About Gerarus
There can be no doubting that the fossil record has provided us with knowledge of some extremely cool organisms. The funny thing is, not all of these extremely cool organisms are very well known. Most popular books on extinct animals tend to select from the same relatively small pool - dinosaurs, ammonites, maybe a trilobite or two. But there are other organisms that one would think would be the stuff of celebrity, but which get almost no screen-time at all. Take Gerarus, for instance - an animal so cool that I've used its name for my own e-mail address. Gerarus is one of the most abundant of Carboniferous insects - specimens have been recovered from almost all major terrestrial deposits of this time, including localities such as Mazon Creek in Illinois and Commentry in France (Béthoux & Briggs, 2008). It's a fairly large insect - some species had wingspans of over ten centimetres. But, beyond all this, the really awesome thing about this critter was that it looked like this:
Reconstruction of Gerarus danielsi from Burnham (1983).
Or in other words, like the unholy offspring of a mantis and a medieval mace. Gerarus was the proud owner of an inflated thorax, liberally studded with prominent don't-f***-with-me spines up to a millimetre in length. Wings of different individuals were notably variable in their venation patterns, suggesting relaxed selectional pressure, and this together with the shift in weight that would have resulted from the hypertrophied thorax suggest that Gerarus was probably not a very active flier (Béthoux & Nel, 2003). Instead, it would have clambered on vegetation like a stick insect, relying primarily on its spines to dissuade potential predators. If that wasn't enough, it could escape by jumping and using its wings as passive gliding planes.
The aforementioned variability of Gerarus and the other members of the family Geraridae led to earlier authors describing nearly every specimen as a separate species. Many of these were synonymised by Burnham (1983) in her review of the family, but it is quite possible that the group is still over-split. Initially, gerarids were included in the "Protorthoptera", an unabashedly paraphyletic or polyphyletic grouping of Palaeozoic polyneopteran-grade insects that was believed to be ancestral to such modern groups as cockroaches, crickets and stick insects, and possibly even to all other recent neopteran insects. When some more specific affinity was hypothesised, it was usually to the Orthoptera (crickets and grasshoppers). This hypothesis was challenged by Kukalová-Peck and Brauckmann (1992), who identified an expanded clypeus in Gerarus (the clypeus is the front part of an insect's head). This, together with certain features of the wing venation, lead them to position Gerarus closer to the Paraneoptera, the group including Psocoptera (booklice) and Hemiptera (bugs). Even more notably, they also identified exites on Gerarus' legs.
Figure of Gerarus danielsi specimen from Kukalová-Peck & Brauckmann (1992), as reproduced in Béthoux & Briggs (2008), showing exites attached to the legs.
Kukalová-Peck is best known for her theories on the origin of insect wings. Many fossil arthropods, and modern crustaceans, possess branched legs, and Kukalová-Peck holds that ancestral insects also possessed such legs, with the wings developed from side-branches (exites) that have become dissociated from the legs and moved closer to the top of the thorax. This contrasts with the earlier idea that insect wings were derived from dorsolateral lobes of the thorax itself. Kukalová-Peck's model has certainly got some points in its favour - it avoids the difficulty of a transition from a fixed lateral lobe to a mobile, articulated wing, and genetic studies have shown that similar genes are involved in the development of Drosophila wings as in that of crustacean gills (which are undoubtedly derived from exites). Kukalová-Peck also identified the presence of exites in a number of fossil insects as further support for her model (Kukalová-Peck, 1987).
However, there are a couple of stumbling blocks. Firstly, those fossil insects on which exites have been identified are phylogenetically nested among modern insects with unbranched legs, which would require the convergent loss of exites in a number of independent lineages (not impossible - exite loss seems to be directly connected to adaptation to life on land for arthropods). Secondly, and perhaps more damningly, some of Kukalová-Peck's reconstructions have been accused of (shall we say) a certain excess of imagination. Béthoux & Nel (2003) re-interpreted the wing venation of Gerarus, and found that it did not possess the features cited by Kukalová-Peck & Brauckmann (1992) as indicating paraneopteran relationships. That still left the expanded clypeus and the exites, but those little details were re-interpreted by Béthoux & Briggs (2008) as artefacts seemingly produced by over-enthusiastic preparation. The current indication is that Gerarus is a member of the Panorthoptera, the clade including Orthoptera plus the extinct orders Titanoptera and Caloneurodea. A close relationship between Geraridae and Titanoptera, enormous grasshopper-like insects, was popular for a while, but was rejected by Béthoux (2007)*. The exact affinities of Gerarus still await elucidation.
*Some day I may do a review of Béthoux (2007), a paper which may or may not constitute a glimpse into the fiery depths of hell. Right now, I haven't the strength.
REFERENCES
Béthoux, O. 2007. Cladotypic taxonomy applied: titanopterans are orthopterans. Arthropod Systematics and Phylogeny 65 (2): 135-156.
Béthoux, O., & D. E. G. Briggs. 2008. How Gerarus lost its head: stem-group Orthoptera and Paraneoptera revisited. Systematic Entomology 33 (3): 529-547.
Béthoux, O., & A. Nel. 2003. Wing venation morphology and variability of Gerarus fischeri (Brongniart, 1885) sensu Burnham (Panorthoptera; Upper Carboniferous, Commentry, France), with inferences on flight performance. Organisms Diversity & Evolution 3 (3): 173-183.
Burnham, L. 1983. Studies on Upper Carboniferous insects: I. The Geraridae (order Protorthoptera). Psyche 90 (1-2): 1-57.
Kukalová-Peck, J. 1987. New Carboniferous Diplura, Monura, and Thysanura, the hexapod ground plan, and the role of thoracic side lobes in the origin of wings (Insecta). Canadian Journal of Zoology 65: 2327-2345.
Kukalová-Peck, J., & C. Brauckmann. 1992. Most Paleozoic Protorthoptera are ancestral hemipteroids: major wing braces as clues to a new phylogeny of Neoptera (Insecta). Canadian Journal of Zoology 70: 2452–2473.
Or in other words, like the unholy offspring of a mantis and a medieval mace. Gerarus was the proud owner of an inflated thorax, liberally studded with prominent don't-f***-with-me spines up to a millimetre in length. Wings of different individuals were notably variable in their venation patterns, suggesting relaxed selectional pressure, and this together with the shift in weight that would have resulted from the hypertrophied thorax suggest that Gerarus was probably not a very active flier (Béthoux & Nel, 2003). Instead, it would have clambered on vegetation like a stick insect, relying primarily on its spines to dissuade potential predators. If that wasn't enough, it could escape by jumping and using its wings as passive gliding planes.
The aforementioned variability of Gerarus and the other members of the family Geraridae led to earlier authors describing nearly every specimen as a separate species. Many of these were synonymised by Burnham (1983) in her review of the family, but it is quite possible that the group is still over-split. Initially, gerarids were included in the "Protorthoptera", an unabashedly paraphyletic or polyphyletic grouping of Palaeozoic polyneopteran-grade insects that was believed to be ancestral to such modern groups as cockroaches, crickets and stick insects, and possibly even to all other recent neopteran insects. When some more specific affinity was hypothesised, it was usually to the Orthoptera (crickets and grasshoppers). This hypothesis was challenged by Kukalová-Peck and Brauckmann (1992), who identified an expanded clypeus in Gerarus (the clypeus is the front part of an insect's head). This, together with certain features of the wing venation, lead them to position Gerarus closer to the Paraneoptera, the group including Psocoptera (booklice) and Hemiptera (bugs). Even more notably, they also identified exites on Gerarus' legs.
Kukalová-Peck is best known for her theories on the origin of insect wings. Many fossil arthropods, and modern crustaceans, possess branched legs, and Kukalová-Peck holds that ancestral insects also possessed such legs, with the wings developed from side-branches (exites) that have become dissociated from the legs and moved closer to the top of the thorax. This contrasts with the earlier idea that insect wings were derived from dorsolateral lobes of the thorax itself. Kukalová-Peck's model has certainly got some points in its favour - it avoids the difficulty of a transition from a fixed lateral lobe to a mobile, articulated wing, and genetic studies have shown that similar genes are involved in the development of Drosophila wings as in that of crustacean gills (which are undoubtedly derived from exites). Kukalová-Peck also identified the presence of exites in a number of fossil insects as further support for her model (Kukalová-Peck, 1987).
However, there are a couple of stumbling blocks. Firstly, those fossil insects on which exites have been identified are phylogenetically nested among modern insects with unbranched legs, which would require the convergent loss of exites in a number of independent lineages (not impossible - exite loss seems to be directly connected to adaptation to life on land for arthropods). Secondly, and perhaps more damningly, some of Kukalová-Peck's reconstructions have been accused of (shall we say) a certain excess of imagination. Béthoux & Nel (2003) re-interpreted the wing venation of Gerarus, and found that it did not possess the features cited by Kukalová-Peck & Brauckmann (1992) as indicating paraneopteran relationships. That still left the expanded clypeus and the exites, but those little details were re-interpreted by Béthoux & Briggs (2008) as artefacts seemingly produced by over-enthusiastic preparation. The current indication is that Gerarus is a member of the Panorthoptera, the clade including Orthoptera plus the extinct orders Titanoptera and Caloneurodea. A close relationship between Geraridae and Titanoptera, enormous grasshopper-like insects, was popular for a while, but was rejected by Béthoux (2007)*. The exact affinities of Gerarus still await elucidation.
*Some day I may do a review of Béthoux (2007), a paper which may or may not constitute a glimpse into the fiery depths of hell. Right now, I haven't the strength.
REFERENCES
Béthoux, O. 2007. Cladotypic taxonomy applied: titanopterans are orthopterans. Arthropod Systematics and Phylogeny 65 (2): 135-156.
Béthoux, O., & D. E. G. Briggs. 2008. How Gerarus lost its head: stem-group Orthoptera and Paraneoptera revisited. Systematic Entomology 33 (3): 529-547.
Béthoux, O., & A. Nel. 2003. Wing venation morphology and variability of Gerarus fischeri (Brongniart, 1885) sensu Burnham (Panorthoptera; Upper Carboniferous, Commentry, France), with inferences on flight performance. Organisms Diversity & Evolution 3 (3): 173-183.
Burnham, L. 1983. Studies on Upper Carboniferous insects: I. The Geraridae (order Protorthoptera). Psyche 90 (1-2): 1-57.
Kukalová-Peck, J. 1987. New Carboniferous Diplura, Monura, and Thysanura, the hexapod ground plan, and the role of thoracic side lobes in the origin of wings (Insecta). Canadian Journal of Zoology 65: 2327-2345.
Kukalová-Peck, J., & C. Brauckmann. 1992. Most Paleozoic Protorthoptera are ancestral hemipteroids: major wing braces as clues to a new phylogeny of Neoptera (Insecta). Canadian Journal of Zoology 70: 2452–2473.
In Which I Blather On Elsewhere
A few weeks ago, Ava of The Reef Tank asked if I would mind answering a few questions for an e-mail interview. Yesterday, I finally got off my backside and sent my answers back to her. You can read the results here.
Stop Giggling (Taxon of the Week: Fartulum)
It has to be admitted that some organisms have rather unfairly copped it when it comes to the names that biologists have chosen to bestow upon them. There are birds called Turdus and Arses, a beetle called Dermestes haemorrhoidalis, even the fungus Rectipilus doesn't sound entirely comfortable. Compared to those unfortunates, today's subject perhaps got off lightly. Still, I don't think I would want to be known as Fartulum.
Fartulum is a taxon in the gastropod family Caecidae. Depending on where you look, it's treated as either its own genus or a subgenus of the genus Caecum (ranking issues again, not really important). Species of Fartulum are distinguished from other species of Caecum or closely related genera by their combination of a cap-shaped apical plug (more on that in a moment) and perfectly smooth mature shell without the rings or ridges of other caecids.
Caecids are one of the more distinctive groups of gastropods. They belong to the superfamily Rissooidea, so are closely related to families with periwinkle-type shells such as Rissoidae and Hydrobiidae, but quite honestly you wouldn't know it to look at them. Mind you, first you'd have to be looking at them, and not many people do that. Not because they're uncommon, but because they're tiny. Many would be pushing it to get past two millimetres. Even if you were sharp-sighted enough to spot a caecid, you might dismiss it as a fragment of something else. Caecids start out life as a flat-spiralling shell, but after a couple of turns the whorls open up and the caecid leaves its tight spiral (Carpenter, 1861). In Caecum and its subgenera or related genera, the growing gastropod then produces an apical plug with which it seals off the upper part of the shell, so the living animal is restricted to the anterior section. With no internal tissue holding it in place, the forsaken spire breaks off, so the mature caecid is a short, slightly curved tube, open at one end and plugged at the other (Carpenter, 1861, described Fartulum specimens as looking like "tiny sausages"). As the caecid continues to secrete new shell at the front, it draws forward the plug at the back and continues to shed old shell.
Caecids are detritivores, and live buried in marine sediment, or among sponges or algae. Despite their obscurity, they are far from uncommon. For instance, an ecological survey of the intertidal zone at Mazatlán Bay on the Pacific coast of Mexico by Olabarria et al. (2001) found Fartulum to be the most abundant deposit-feeder there by a fairly significant margin.
REFERENCES
Carpenter, P. P. 1861. Lectures on Mollusca, or "Shell-fish" and their Allies. Prepared for the Smithsonian Institution. Congressional Globe Office: Washington.
Olabarria, C., J. L. Carballo & C. Vega. 2001. Spatio-temporal changes in the trophic structure of rocky intertidal mollusc assemblages on a tropical shore. Ciencias Marinas 27 (2): 235-254.
Further Details
Not so long ago, I remarked that I could be found on Facebook under my own name. I have since had it pointed out that as "Christopher Taylor" is hardly the most individual of names out there, I couldn't really be found amongst the 500+ other Christopher Taylors. So alternatively, if you want to find me, try using my e-mail (gerarus at westnet.com.au). Or, funnily enough, searching for "Opiliones" brings me up as one of the results too.
Apropos of none of which, but because I needed to fill out the post somehow, here is a Flight of the Conchords clip:
Apropos of none of which, but because I needed to fill out the post somehow, here is a Flight of the Conchords clip:
Crossing the Algal Divide
This post is the direct result of a brief exchange in the comments to an earlier post which has nothing in itself to do with this one. Isn't it funny how tangents work?
Glaucocystis, a member of the primary chloroplast-carrying glaucophytes. Photo by Jason Oyadomari.
It has become pretty much universally acknowledged that at least two of the organelles found in eukaryotic cells, mitochondria and chloroplasts, are derived from endosymbiotic bacteria that progressively gave up more and more of their vital functions to their host cells until they became inextricably linked to them. Mitochondria are probably derived from Alphaproteobacteria (Gray et al., 2004), while chloroplasts are certainly derived from Cyanobacteria. Endosymbiotic origins have been suggested for other organelles, most notably the eukaryotic flagellum, but have not reached the same level of acceptance. While a number of eukaryotes lacking mitochondria are found in the world today, the weight of current evidence suggests that most if not all are descended from mitochondria-carrying ancestors, and the origin of the mitochondrion pre-dates the known eukaryote crown group. The origin of the chloroplast, however, is not quite so simple.
Cryptomonas, another unicellular alga from a different group, the cryptomonads. Photo from here.
The chloroplast was undoubtedly a later innovation than the mitochondrion. As I've alluded to before, the basalmost division in eukaryotes currently seems to be between unikonts (including animals, fungi and amoebozoans) on one side and bikonts (plants and most other protists) on the other. All eukaryotes with chloroplasts are bikonts (with the exception of sequestered chloroplasts in some marine molluscs and flatworms), so chloroplasts at least post-date this division. Unfortunately, bikonts are a much more disparate bunch than unikonts, and our understanding of how the various major groups of bikonts are related to each other is correspondingly less. Among the bikonts, chloroplasts or clear chloroplast derivatives are found in twelve well-supported monophyletic groups (as a cautious maximum). However, different groups have chloroplasts with different physiologies and ultrastructures, indicating different modes of origin. Some groups have what are called primary chloroplasts, derived directly from endosymbiotic cyanobacteria. Primary chloroplasts have two membranes separating the host cell and chloroplast cytoplasm, corresponding to the two cell membranes of a free-living cyanobacterium. Most cyanobacteria contain a single type of chlorophyll, chlorophyll a, and so do the primary chloroplasts of glaucophytes* (a small group of unicellular algae), rhodophytes (red algae) and the shelled amoeboid Paulinella. The fourth group of eukaryotes with primary chloroplasts, Viridiplantae (green algae and land plants), differ in having two types of chlorophyll, both the original a and an additional form called chlorophyll b**. Glaucophyte, rhodophyte and viridiplantaean chloroplasts share a number of genetic signatures absent from cyanobacteria, suggesting that their chloroplasts are derived from a single endosymbiotic event (Kim & Graham, 2008). The chloroplast of Paulinella, on the other hand, is more similar to a cyanobacterium, and Paulinella has clear and close non-photosynthetic relatives among the group of unicellular protists known as Cercozoa. Paulinella is therefore believed to have acquired its chloroplast recently and completely independently of the other groups.
*As an intriguing aside, it was long debated whether it was more appropriate to regard the photosynthetic enclusions in glaucophytes as "chloroplasts" or "endosymbiotic cyanobacteria", and a number of glaucophyte chloroplasts were given names as taxa in their own right.
*Just to confuse matters, there are also three species of cyanobacteria that possess chlorophyll b. Current indications are that these species are not closely related to Viridiplantae chloroplasts - nor, indeed, are they closely related to each other. The odd scattered distribution of chlorophyll b remains as yet completely unexplained.
Diagram of the origin of secondary chloroplasts in chlorarachniophytes through the engulfment of one eukaryote by another. From ToLWeb.
The remaining groups of photosynthetic eukaryotes, in contrast, have what are called secondary chloroplasts (or, in a few cases, tertiary or even quaternary chloroplasts). Secondary chloroplasts have three or four membranes surrounding them, and are not derived directly from a cyanobacterium, but from a eukaryotic alga containing a primary chloroplast. In those secondary chloroplasts with four membranes, then, the membranes represent the two membranes of the primary chloroplast, the outer cell membrane of the endosymbiotic eukaryotic alga, and the membrane surrounding the vacuole in which the secondary host contained its endosymbiont. Clear support for this complicated origin can be seen in the two secondary-chloroplast groups, the amoeboid chlorarachniophytes and the flagellate crytomonads, where a small dark mass sits wedged between the second and third membranes. This mass contains DNA, and is nothing less than the degraded remnants of the endosymbiotic alga's original nucleus.
Coccolithophores, shelled algae of the Haptophyta. Image from here.
Two groups of secondary-chloroplast algae, the chlorarachniophytes and the euglenoids (Euglena is probably about the most commonly-illustrated flagellate in any textbook), possess chlorophylls a and b, indicating an ancestor among the Viridiplantae for their chloroplasts. For the remaining groups, phylogenetic analyses indicate a rhodophyte origin for their chloroplasts. The recently discovered Chromera only has chlorophyll a, like a rhodophyte, while Chromera's relatives in the parasitic Coccidiomorpha (a subgroup of the Sporozoa) possess chlorophyll-less chloroplast derivatives. The remaining four groups - cryptomonads, haptophytes (coccolithophores), ochrophytes (which include brown and golden algae and diatoms) and dinoflagellates - possess two types of chlorophyll, a and a form called chlorophyll c that is unique to these taxa.
The big question hovering over eukaryote phylogenetics is how many times these secondary endosymbioses occurred. One of the most prolific authors in this field has been the British researcher Tom Cavalier-Smith. Cavalier-Smith's writings can induce feelings of great admiration or extreme loathing (sometimes both over the course of a single page)*, but one certainly can't go very far without coming up against them. A lot of Cavalier-Smith's views (some of them since adjusted) were summarised in what was published in 2002 as two papers (Cavalier-Smith, 2002a, 2002b) but should really be read as one single gigantic über-paper on the origins of life, the universe and everything (well, not the universe, but you get the idea). Using a combination of molecular and morphological interpretations, Cavalier-Smith divided the bikonts into five major clades, all but one including both photosynthetic and non-photosynthetic major subgroups - Excavata (including euglenoids, among others), Rhizaria (to which belong chlorarachniophytes and Paulinella, as well as foraminifera and radiolarians), Plantae (the remaining primary-chloroplast organisms), Alveolata (dinoflagellates, sporozoans and ciliates) and Chromista (cryptomonads, haptophytes and heterokonts - the last includes the ochrophytes). He further proposed that the Alveolata and Chromista together formed a clade called chromalveolates, uniting all the chlorophyll c-containing organisms. Supposedly, the rhodophyte endosymbiosis giving rise to the chromalveolate chloroplast happened just once, and the non-photosynthetic chromalveolates are derived from ancestors that lost their chloroplasts.
*At least in the late 1990s and the early 2000s, a rough indication of the amount of ire that Cavalier-Smith's publications generated in some circles could be gained by scanning the works of other protistologists and noting the lengths some of them went to not to cite Cavalier-Smith.
Paulinella. This genus is the only eukaryote lineage to have acquired its chloroplasts separately from the archaeplastid lineage. Photo from here.
A major factor in Cavalier-Smith's proposals has been the idea that chloroplast acquisition is far more difficult than chloroplast loss, because gaining a working chloroplast requires not only the endosymbiont but the evolution of appropriate molecular channels for transporting metabolites between the endosymbiont and the host cell, so the phylogeny that minimises the number of chloroplast acquisitions is most likely to be true (as an extreme example, in 1999 he also suggested that Excavata and Rhizaria formed a clade derived from a single green algal endosymbiosis, which the resulting chloroplast lost in all members of both clades except chlorarachniophytes and euglenoids. Because chlorarachniophytes and euglenoids are both nested reasonably deeply within their respective clades, necessitating a fairly large number of chloroplast losses in this scenario, nobody except for Cavalier-Smith himself seems to have given it a huge amount of credence). Other researchers, on the other hand, hold the opposite view - that chloroplasts perform such a significant role in their host cells that losing them would be a Very Bad Thing - and point to the fact that many photosynthetic groups have clear closest relatives among non-photosynthetic groups. Unfortunately, most phylogenetic analyses in this field have lacked strong resolution or support, probably simply due to the incredibly long time since the lineages diverged.
So where do things stand now? In the last couple of years, analyses of sometimes quite huge amounts of data have been released. Of Cavalier-Smith's (2002b) five groups, the Rhizaria and Alveolata have continued to receive support from almost all angles. The Excavata continue to cause a bit of hemming and hawing (though Hampl et al., 2009, recently presented the first molecular analysis to support excavate monophyly), but with only one photosynthetic subgroup they're not really relevant to the current discussion anyway. The monophyly of the Plantae (renamed Archaeplastida in the eukaryote classification of Adl et al., 2005, to avoid the confusion of the many different uses of the name "Plantae") is at a bit of a draw - Patron et al. (2007) and Burki et al. (in press, 2008), for instance, found it as monophyletic, but Kim & Graham (2008) and Hampl et al. (2009) did not. None of the recent analyses, however, have found a monophyletic Chromista. The cryptomonads and haptophytes look to form a clade that may be close to (Patron et al., 2007; Burki et al., in press, 2008) or even within (Kim & Graham, 2008; Hampl et al., 2009) the archaeplastids. The heterokonts seem to form a clade (with a certain degree of irony) with the alveolates - which brings up the possibility that, depending on how you choose to use the names, "chromalveolates" may be monophyletic even if "chromists" are not. A surprising result of a number of recent analyses (including most of the ones cited above) is that this reduced chromalveolate clade may be sister to the Rhizaria.
As shown in the figure above from Bodył et al (2009) summarising all this, this implies a number more chloroplast origins than Cavalier-Smith's model. Does this vindicate those who hold that chloroplast acquisition is easier than chloroplast loss? Well, as often happens in biology, there is a third possibility. As well as chloroplast gain and chloroplast loss, there is also chloroplast replacement. Dinoflagellates, the one group of eukaryotes that never manage to do anything sensibly, include some members with secondary rhodophyte-derived chloroplasts, and others with tertiary chloroplasts that seem to be derived from haptophytes. It seems that these serial hosts have shucked out their original secondary chloroplasts in favour of a new endosymbiont. Chloroplast replacement sidesteps some of the theoretical difficulties of acquiring a chloroplast entirely de novo, because the host already possesses the biochemical pathways to communicate with its new chloroplast. If the cryptomonad-haptophyte clade is nested within archaeplastids, as indicated by some phylogenies, this may represent a case of chloroplast replacement rather than chloroplast gain.
REFERENCES
Adl, S. M., A. G. B. Simpson, M. A. Farmer, R. A. Andersen, O. R. Andersen, J. R. Barta, S. S. Bowser, G. Brugerolle, R. A. Fensome, S. Fredericq, T. Y. James, S. Karpov, P. Krugens, J. Krug, C. E. Lane, L. A. Lewis, J. Lodge, D. H. Lynn, D. G. Mann, R. M. McCourt, L. Mendoza, Ø. Moestrup, S. E. Mozley-Standridge, T. A. Narad, C. A. Shearer, A. V. Smirnov, F. W. Spiegel & M. F. J. R. Taylor. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology 52: 399-451.
Bodył, A., J. W. Stiller & P. Mackiewicz. 2009. Chromalveolate plastids: direct descent or multiple endosymbioses? Trends in Ecology and Evolution 24 (3): 119-121.
Burki, F., K. Shalchian-Tabrizi & J. Pawlowski. in press, 2008. Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes. Biology Letters.
Cavalier-Smith, T. 1999. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. Journal of Eukaryotic Microbiology 46 (4): 347-366.
Cavalier-Smith, T. 2002a. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7-76.
Cavalier-Smith, T. 2002b. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International Journal of Systematic and Evolutionary Microbiology 52: 297-354.
Gray, M. W., B. F. Lang & G. Burger. 2004. Mitochondria of protists. Annual Review of Genetics 38: 477-524.
Hampl, V., L. Hug, J. W. Leigh, J. B. Dacks, B. F. Lang, A. G. B. Simpson & A. J. Roger. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proceedings of the National Academy of Sciences of the USA 106 (10): 3859-3864.
Kim, E., & L. E. Graham. 2008. EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. PLoS ONE 3(7): e2621.
Patron, N. J., Y. Inagaki & P. J. Keeling. 2007. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Current Biology 17: 887-891.
It has become pretty much universally acknowledged that at least two of the organelles found in eukaryotic cells, mitochondria and chloroplasts, are derived from endosymbiotic bacteria that progressively gave up more and more of their vital functions to their host cells until they became inextricably linked to them. Mitochondria are probably derived from Alphaproteobacteria (Gray et al., 2004), while chloroplasts are certainly derived from Cyanobacteria. Endosymbiotic origins have been suggested for other organelles, most notably the eukaryotic flagellum, but have not reached the same level of acceptance. While a number of eukaryotes lacking mitochondria are found in the world today, the weight of current evidence suggests that most if not all are descended from mitochondria-carrying ancestors, and the origin of the mitochondrion pre-dates the known eukaryote crown group. The origin of the chloroplast, however, is not quite so simple.
The chloroplast was undoubtedly a later innovation than the mitochondrion. As I've alluded to before, the basalmost division in eukaryotes currently seems to be between unikonts (including animals, fungi and amoebozoans) on one side and bikonts (plants and most other protists) on the other. All eukaryotes with chloroplasts are bikonts (with the exception of sequestered chloroplasts in some marine molluscs and flatworms), so chloroplasts at least post-date this division. Unfortunately, bikonts are a much more disparate bunch than unikonts, and our understanding of how the various major groups of bikonts are related to each other is correspondingly less. Among the bikonts, chloroplasts or clear chloroplast derivatives are found in twelve well-supported monophyletic groups (as a cautious maximum). However, different groups have chloroplasts with different physiologies and ultrastructures, indicating different modes of origin. Some groups have what are called primary chloroplasts, derived directly from endosymbiotic cyanobacteria. Primary chloroplasts have two membranes separating the host cell and chloroplast cytoplasm, corresponding to the two cell membranes of a free-living cyanobacterium. Most cyanobacteria contain a single type of chlorophyll, chlorophyll a, and so do the primary chloroplasts of glaucophytes* (a small group of unicellular algae), rhodophytes (red algae) and the shelled amoeboid Paulinella. The fourth group of eukaryotes with primary chloroplasts, Viridiplantae (green algae and land plants), differ in having two types of chlorophyll, both the original a and an additional form called chlorophyll b**. Glaucophyte, rhodophyte and viridiplantaean chloroplasts share a number of genetic signatures absent from cyanobacteria, suggesting that their chloroplasts are derived from a single endosymbiotic event (Kim & Graham, 2008). The chloroplast of Paulinella, on the other hand, is more similar to a cyanobacterium, and Paulinella has clear and close non-photosynthetic relatives among the group of unicellular protists known as Cercozoa. Paulinella is therefore believed to have acquired its chloroplast recently and completely independently of the other groups.
*As an intriguing aside, it was long debated whether it was more appropriate to regard the photosynthetic enclusions in glaucophytes as "chloroplasts" or "endosymbiotic cyanobacteria", and a number of glaucophyte chloroplasts were given names as taxa in their own right.
*Just to confuse matters, there are also three species of cyanobacteria that possess chlorophyll b. Current indications are that these species are not closely related to Viridiplantae chloroplasts - nor, indeed, are they closely related to each other. The odd scattered distribution of chlorophyll b remains as yet completely unexplained.
The remaining groups of photosynthetic eukaryotes, in contrast, have what are called secondary chloroplasts (or, in a few cases, tertiary or even quaternary chloroplasts). Secondary chloroplasts have three or four membranes surrounding them, and are not derived directly from a cyanobacterium, but from a eukaryotic alga containing a primary chloroplast. In those secondary chloroplasts with four membranes, then, the membranes represent the two membranes of the primary chloroplast, the outer cell membrane of the endosymbiotic eukaryotic alga, and the membrane surrounding the vacuole in which the secondary host contained its endosymbiont. Clear support for this complicated origin can be seen in the two secondary-chloroplast groups, the amoeboid chlorarachniophytes and the flagellate crytomonads, where a small dark mass sits wedged between the second and third membranes. This mass contains DNA, and is nothing less than the degraded remnants of the endosymbiotic alga's original nucleus.
Two groups of secondary-chloroplast algae, the chlorarachniophytes and the euglenoids (Euglena is probably about the most commonly-illustrated flagellate in any textbook), possess chlorophylls a and b, indicating an ancestor among the Viridiplantae for their chloroplasts. For the remaining groups, phylogenetic analyses indicate a rhodophyte origin for their chloroplasts. The recently discovered Chromera only has chlorophyll a, like a rhodophyte, while Chromera's relatives in the parasitic Coccidiomorpha (a subgroup of the Sporozoa) possess chlorophyll-less chloroplast derivatives. The remaining four groups - cryptomonads, haptophytes (coccolithophores), ochrophytes (which include brown and golden algae and diatoms) and dinoflagellates - possess two types of chlorophyll, a and a form called chlorophyll c that is unique to these taxa.
The big question hovering over eukaryote phylogenetics is how many times these secondary endosymbioses occurred. One of the most prolific authors in this field has been the British researcher Tom Cavalier-Smith. Cavalier-Smith's writings can induce feelings of great admiration or extreme loathing (sometimes both over the course of a single page)*, but one certainly can't go very far without coming up against them. A lot of Cavalier-Smith's views (some of them since adjusted) were summarised in what was published in 2002 as two papers (Cavalier-Smith, 2002a, 2002b) but should really be read as one single gigantic über-paper on the origins of life, the universe and everything (well, not the universe, but you get the idea). Using a combination of molecular and morphological interpretations, Cavalier-Smith divided the bikonts into five major clades, all but one including both photosynthetic and non-photosynthetic major subgroups - Excavata (including euglenoids, among others), Rhizaria (to which belong chlorarachniophytes and Paulinella, as well as foraminifera and radiolarians), Plantae (the remaining primary-chloroplast organisms), Alveolata (dinoflagellates, sporozoans and ciliates) and Chromista (cryptomonads, haptophytes and heterokonts - the last includes the ochrophytes). He further proposed that the Alveolata and Chromista together formed a clade called chromalveolates, uniting all the chlorophyll c-containing organisms. Supposedly, the rhodophyte endosymbiosis giving rise to the chromalveolate chloroplast happened just once, and the non-photosynthetic chromalveolates are derived from ancestors that lost their chloroplasts.
*At least in the late 1990s and the early 2000s, a rough indication of the amount of ire that Cavalier-Smith's publications generated in some circles could be gained by scanning the works of other protistologists and noting the lengths some of them went to not to cite Cavalier-Smith.
A major factor in Cavalier-Smith's proposals has been the idea that chloroplast acquisition is far more difficult than chloroplast loss, because gaining a working chloroplast requires not only the endosymbiont but the evolution of appropriate molecular channels for transporting metabolites between the endosymbiont and the host cell, so the phylogeny that minimises the number of chloroplast acquisitions is most likely to be true (as an extreme example, in 1999 he also suggested that Excavata and Rhizaria formed a clade derived from a single green algal endosymbiosis, which the resulting chloroplast lost in all members of both clades except chlorarachniophytes and euglenoids. Because chlorarachniophytes and euglenoids are both nested reasonably deeply within their respective clades, necessitating a fairly large number of chloroplast losses in this scenario, nobody except for Cavalier-Smith himself seems to have given it a huge amount of credence). Other researchers, on the other hand, hold the opposite view - that chloroplasts perform such a significant role in their host cells that losing them would be a Very Bad Thing - and point to the fact that many photosynthetic groups have clear closest relatives among non-photosynthetic groups. Unfortunately, most phylogenetic analyses in this field have lacked strong resolution or support, probably simply due to the incredibly long time since the lineages diverged.
So where do things stand now? In the last couple of years, analyses of sometimes quite huge amounts of data have been released. Of Cavalier-Smith's (2002b) five groups, the Rhizaria and Alveolata have continued to receive support from almost all angles. The Excavata continue to cause a bit of hemming and hawing (though Hampl et al., 2009, recently presented the first molecular analysis to support excavate monophyly), but with only one photosynthetic subgroup they're not really relevant to the current discussion anyway. The monophyly of the Plantae (renamed Archaeplastida in the eukaryote classification of Adl et al., 2005, to avoid the confusion of the many different uses of the name "Plantae") is at a bit of a draw - Patron et al. (2007) and Burki et al. (in press, 2008), for instance, found it as monophyletic, but Kim & Graham (2008) and Hampl et al. (2009) did not. None of the recent analyses, however, have found a monophyletic Chromista. The cryptomonads and haptophytes look to form a clade that may be close to (Patron et al., 2007; Burki et al., in press, 2008) or even within (Kim & Graham, 2008; Hampl et al., 2009) the archaeplastids. The heterokonts seem to form a clade (with a certain degree of irony) with the alveolates - which brings up the possibility that, depending on how you choose to use the names, "chromalveolates" may be monophyletic even if "chromists" are not. A surprising result of a number of recent analyses (including most of the ones cited above) is that this reduced chromalveolate clade may be sister to the Rhizaria.
As shown in the figure above from Bodył et al (2009) summarising all this, this implies a number more chloroplast origins than Cavalier-Smith's model. Does this vindicate those who hold that chloroplast acquisition is easier than chloroplast loss? Well, as often happens in biology, there is a third possibility. As well as chloroplast gain and chloroplast loss, there is also chloroplast replacement. Dinoflagellates, the one group of eukaryotes that never manage to do anything sensibly, include some members with secondary rhodophyte-derived chloroplasts, and others with tertiary chloroplasts that seem to be derived from haptophytes. It seems that these serial hosts have shucked out their original secondary chloroplasts in favour of a new endosymbiont. Chloroplast replacement sidesteps some of the theoretical difficulties of acquiring a chloroplast entirely de novo, because the host already possesses the biochemical pathways to communicate with its new chloroplast. If the cryptomonad-haptophyte clade is nested within archaeplastids, as indicated by some phylogenies, this may represent a case of chloroplast replacement rather than chloroplast gain.
REFERENCES
Adl, S. M., A. G. B. Simpson, M. A. Farmer, R. A. Andersen, O. R. Andersen, J. R. Barta, S. S. Bowser, G. Brugerolle, R. A. Fensome, S. Fredericq, T. Y. James, S. Karpov, P. Krugens, J. Krug, C. E. Lane, L. A. Lewis, J. Lodge, D. H. Lynn, D. G. Mann, R. M. McCourt, L. Mendoza, Ø. Moestrup, S. E. Mozley-Standridge, T. A. Narad, C. A. Shearer, A. V. Smirnov, F. W. Spiegel & M. F. J. R. Taylor. 2005. The new higher level classification of eukaryotes with emphasis on the taxonomy of protists. Journal of Eukaryotic Microbiology 52: 399-451.
Bodył, A., J. W. Stiller & P. Mackiewicz. 2009. Chromalveolate plastids: direct descent or multiple endosymbioses? Trends in Ecology and Evolution 24 (3): 119-121.
Burki, F., K. Shalchian-Tabrizi & J. Pawlowski. in press, 2008. Phylogenomics reveals a new ‘megagroup’ including most photosynthetic eukaryotes. Biology Letters.
Cavalier-Smith, T. 1999. Principles of protein and lipid targeting in secondary symbiogenesis: euglenoid, dinoflagellate, and sporozoan plastid origins and the eukaryote family tree. Journal of Eukaryotic Microbiology 46 (4): 347-366.
Cavalier-Smith, T. 2002a. The neomuran origin of archaebacteria, the negibacterial root of the universal tree and bacterial megaclassification. International Journal of Systematic and Evolutionary Microbiology 52: 7-76.
Cavalier-Smith, T. 2002b. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa. International Journal of Systematic and Evolutionary Microbiology 52: 297-354.
Gray, M. W., B. F. Lang & G. Burger. 2004. Mitochondria of protists. Annual Review of Genetics 38: 477-524.
Hampl, V., L. Hug, J. W. Leigh, J. B. Dacks, B. F. Lang, A. G. B. Simpson & A. J. Roger. 2009. Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proceedings of the National Academy of Sciences of the USA 106 (10): 3859-3864.
Kim, E., & L. E. Graham. 2008. EEF2 analysis challenges the monophyly of Archaeplastida and Chromalveolata. PLoS ONE 3(7): e2621.
Patron, N. J., Y. Inagaki & P. J. Keeling. 2007. Multiple gene phylogenies support the monophyly of cryptomonad and haptophyte host lineages. Current Biology 17: 887-891.
Everything You Knew About Mayflies is Wrong (Taxon of the Week: Pisciforma)
Mayflies are one of the most basal, if not the most basal groups of winged insects alive today. The one thing that everyone knows about mayflies is that they only live for a day. This is reflected in their order name Ephemeroptera - "fleeting wing". But like so many other things that "everyone knows", this is complete twaddle. Mayflies do not live for a day. Indeed, by insect standards mayflies often have very long lives - many will live for an entire year, and some will live for as long as three years. The "fleeting" part of their lives is not their life as a whole, but only their time as adults.
Like dragonflies, mayflies spend the juvenile part of their life cycles as aquatic nymphs. They are easily distinguished from the aquatic nymphs of other insect orders by their three long caudal filaments and the leaf-like lateral gills that run down each side of their abdomens. Most mayfly nymphs are herbivorous or detritivorous, but a few are predatory. In contrast, adult mayflies have almost non-existent mouthparts, and do not feed - hence their "brief" lives. Mayflies are also unique in being the only living winged insects to undergo a moult after their wings develop. They first emerge from the water in a form known as the subimago, which soon moults into the final, fully mature imago. Mating usually happens in the imago stage, but there are some species that find themselves unable to wait that long, and begin mating as subimagoes (Grimaldi & Engel, 2005).
The contrast between mayflies' long juvenile lives and brief adult lives highlights a common prejudice to which almost all of us are prone - we tend to think of most animals in terms of their adult forms rather than their juvenile ones. There are a number of reasons for this. One is that we ourselves spend more of our life cycle (if we're lucky) as adults than juveniles. Another is that the adults are usually larger and more visible than the often reclusive juveniles, so we're more likely to notice them. Even working biologists may be prone to this trap - many animals can only be fully identified once they reach adulthood, which leads to the subconcious tendency to dismiss the unidentifiable juveniles as unimportant. But from an ecological perspective, it is the long-term juvenile mayflies that are far more significant than the brief adults. Adulthood in mayflies is simply a coda, a brief interlude to prepare for the next movement. Similarly, one could argue about how appropriate it is to characterise mayflies as flying insects when for so much of their lives they are not, with flight for them having no other purpose than to facilitate the reproductive process.
An influential classification of recent mayflies by McCafferty (1991) divided them into three suborders, Rectracheata, Setisura and Pisciforma, largely on the basis of their tracheal anatomy. Unfortunately, McCafferty did not explicitly refer to the characters on which he based the Pisciforma, other than noting that the name referred to the "minnow-like bodies and actions of the larvae". McCafferty (1991) regarded the Pisciforma and Setisura as forming a clade to the exclusion of the Rectracheata. In contrast, Kluge (2004) used an alternative classification* that more or less united McCafferty's Setisura and Rectracheata into a clade Bidentisetata, with two tooth-like setae on the maxilla (I say more or less because the families involved were not exactly the same), separate from the "Tridentisetata" (effectively McCafferty's original Pisciforma) with three tooth-like setae. Kluge explicitly stated, however, that his Tridentisetata was a taxon of convenience united by plesiomorphies only and probably paraphyletic with regard to the Bidentisetata. Recent molecular analyses have confirmed that the "Pisciforma" are paraphyletic or polyphyletic. Ogden & Whiting (2005) found both Rectracheata and Setisura nested within Pisciforma, and suggested that the fish-like nymphal form was plesiomorphic for all living mayflies and lost on numerous subsequent occasions.
*Very alternative, in fact. Kluge (2004) introduced a new system of nomenclature that attempts to provide an alternative to the rank-based system. Without wanting to go into too many details (for a start, that would require me to actually follow what's going on there, and frankly I haven't got a clue), Kluge's system involves a combination of a type genus plus a suffix indicating a taxon's position in the taxonomic hierarchy. So Arthropoda, for instance, is referred to by Kluge as Araneus/fg7. Seriously.
There is one little detail that I have to mention before ending this post. One characteristic of the wings of living mayflies as a whole is a significant difference in size between the fore- and hindwings, with the forewings significantly larger. This is taken to its extreme in one of the pisciform families, the Baetidae, which are one of the few groups of insects in which the hindwings have been almost entirely lost, reduced to small pair of buds like those of flies.
REFERENCES
Grimaldi, D., & M. S. Engel. 2005. Evolution of the Insects. Cambridge University Press: New York.
Kluge, N. 2004. The Phylogenetic System of Ephemeroptera. Springer.
McCafferty, W. P. 1991. Toward a phylogenetic classification of the Ephemeroptera (Insecta): a commentary on systematics. Annals of the Entomological Society of America 84 (4): 343-360.
Ogden, T. H., & M. F. Whiting. 2005. Phylogeny of Ephemeroptera (mayXies) based on molecular evidence. Molecular Phylogenetics and Evolution 37: 625-643.
Side-issues
Fistly, the new edition of Berry Go Round, the monthly plant carnival, is at Quiche Morraine.
Secondly, because I'm always late to a party, a moment of weakness and ennui lead me to sign up on Facebook. If you want to find me there, I'm under my own name - I haven't the imagination to use a pseudonym.
Secondly, because I'm always late to a party, a moment of weakness and ennui lead me to sign up on Facebook. If you want to find me there, I'm under my own name - I haven't the imagination to use a pseudonym.
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