Catalogue of Organisms

Southern Moss (Taxon of the Week: Ptychomitrium muelleri)

noreply@blogger.com (Christopher Taylor) — Mon, 06 Jul 2009 03:31:00 +0000

There don't seem to be any images of Ptychomitrium muelleri available online, so here's another Ptychomitrium species, P. gardneri from China. Photo by Li Zhang.

Mosses are often treated as the poor relation in plant diversity. Popular presentations of plant evolution often tend to have even more of a Scala Natura-esque slant to them than presentations of animal evolution, and so mosses and other non-vascular plants get glossed over as mere stepping stones to their more upright "descendants", if they even warrant a mention at all. This is, of course, complete rubbish - mosses have a very respectable diversity of species (about 10,000, according to Tree of Life). I've met a few moss researchers over the years, and a more devoted following a taxon could not hope for.

Ptychomitrium muelleri is a haplolepidous moss of the family Ptychomitriaceae (I'll explain what that means in a minute). It grows to a maximum height of one and a half centimetres, and if the type specimens are any indication, prefers to grow on rocks. Ptychomitrium mosses seem to be found more or less worldwide, but Ptychomitrium muelleri itself is found in south-eastern Australia, New Caledonia, southern South America and southernmost Africa. What is interesting about this species' distriution is that it was thought to be endemic to Australia until very recently when Cao et al. (2001) established that species described from each of the other localities were conspecific with P. muelleri. As a result, P. muelleri has what might be described as a classic "Gondwanan" distribution, but I rather doubt that Gondwana had anything to do with it. After all, moss spores are very light and extremely easily dispersed, and surely it is no coincidence that all the localities where P. muelleri can be found lie roughly along the same wind belt.

The diagram of a moss life cycle above has been stole from Palaeos.com. For the nonce, the important details are these - mosses, like other plants, are multicellular at both the haploid and diploid stages of the life cycle, but unlike vascular plants, the larger, dominant stage of the life cycle is the haploid gametophyte. When a female gametophyte is fertilised, the diploid sporophyte remains attached to the gametophyte and grows a spore-filled capsule that eventually breaks open (after the loss of the protective calyptra) to release the spores. Around the mouth of the capsule is a ring of "teeth", the peristome. In basal mosses, the peristome is made up of entire cells, but in the class Bryopsida, the arthrodontous mosses (which includes the larger part of the mosses), the teeth are reduced to cell wall remnants. Most of the bryopsid lineages have two rows of teeth in the peristome, an outer and an inner, but Ptychomitrium belongs to a group called the Haplolepideae or Dicranidae which have only the inner row of teeth. The haplolepidous mosses form a monophyletic clade within the Bryopsida.

Ptychomitrium polyphyllum from Scotland, showing the calyptra on the left capsule and the exposed peristome on the right. Photo from here.

Most of the features separating moss taxa are microscopic and relate to such things as cell arrangement (which is my weaselly method of saying that I don't understand a word of them), but Ptychomitrium is distinguished by having a mitrate calyptra (and those unsure what "mitrate" means might want to look at the Taxon of the Week post of two weeks ago) with characteristic lobes around the lower edge (Hernández-Maqueda et al., 2008, compare it to a Hawaiian skirt). Ptychomitrium muelleri has (amongst other features) lingulate (tongue-shaped, I'm guessing) leaves with smooth margins, and ovoid capsules.

REFERENCES

Cao, T., S. Guo & Y. Zhang. 2001. Distribution of Ptychomitrium muelleri (Bryopsida), with its synonyms. The Bryologist 104 (4): 522-526.

Hernández-Maqueda, R., D. Quandt, O. Werner & J. Muñoz. 2008. Phylogeny and classification of the Grimmiaceae/Ptychomitriaceae complex (Bryophyta) inferred from cpDNA. Molecular Phylogenetics and Evolution 46 (3): 863-877.

Knocked Off the Perch (Taxon of the Week: Percidae)

noreply@blogger.com (Christopher Taylor) — Fri, 03 Jul 2009 05:22:00 +0000

The rainbow darter, Etheostoma caeruleum, a representative of the North American radiation of small and often colourful freshwater fish known as darters. This species breeds on fast gravel riffles, where pairs mate with the female half buried in the gravel so the eggs are automatically covered over (Reeves, 1907). Photo by Jim McCormac.

Okay, this post has been delayed again. It's been an unusual week, is all I can say. I'd tell you all about, but I have very good reasons to believe that that would be extremely dull.

In earlier posts, I have ranted in a rather esoteric manner about my distaste with the commonly recognised fish order "Perciformes", really a random multi-paraphyletic assemblage of the more generalised members of the clade Percomorpha. In the recent partial reclassification of the Percomorpha by Li et al. (2009), the name "Perciformes" was ditched entirely, and the clade containing the family Percidae was instead called Serraniformes (suggesting, offhand, that some sort of taxonomic karma is dooming this taxon to be associated with confusing names - the family Serranidae as commonly recognised itself seems likely to be polyphyletic, and a number of "serranids" are not guaranteed Serraniformes). But even before the Perciformes of common use were recognised as a wastebasket assemblage (if, indeed, there ever really was such a time), Percidae was always a slightly odd choice for the type family. The Percidae, the perches and darters, are not particularly average Perciformes.

Among the percomorphs, percids are unusual for one main reason - they're almost entirely freshwater (a few European species stray into brackish waters, but only one species - Sander marinus, the estuarine perch of the Black and Caspian Seas - is a permanent resident in them). While the percomorphs have achieved true world dominance in the upper parts of the ocean, including the vast majority of coastal and surface-pelagic fish species, they have never made such significant inroads into fresh water. A few percomorph lineages have been very successful in fresh water, such as the Cichlidae, the Anabantiformes and various members of the Smegmamorpha*. But in contrast to their surface-marine monopoly, percomorphs have to share dominance of the fresh-water environment with members of the clade Otophysi - Cypriniformes, Characiformes and Siluriformes.

*No, honestly, it's a real name.

The zander, Sander lucioperca, a much larger Eurasian percid. Photo from EoL.

The Serraniformes also include the Trachinidae (weevers), the circum-Antarctic notothenioids and the majority of what were the Scorpaeniformes. Relationships within the Serraniformes are yet to be hammered out, but the Percidae probably divide from the others reasonably basally. Ten genera of living Percidae are currently recognised, with more than two hundred species. Phylogenetic analysis of the family by Sloss et al. (2004) recognised three main clades of unresolved relationships - the Holarctic genus Perca, the mostly Eurasian clade of Gymnocephalus plus Luciopercinae (genera Romanichthys, Sander and Zingel, with three species of Sander in North America), and the North American clade of Etheostomatinae (Ammocrypta, Crystallaria, Etheostoma and Percina). [The tenth genus includes the single uncommon species Percarina demidoffi of rivers running into the Black Sea, and was not analysed by Sloss et al. due to lack of material. Percarina was previously classified in the possibly non-monophyletic Percinae* with Perca and Gymnocephalus and differs from most other Percinae in spawning in brackish waters, so establishing its relationships would be very interesting.] While the greater phylogenetic disparity of Percidae is concentrated in the western Palaearctic and the family is believed to have originated in that area, the greater diversity of species is definitely found in North America. Well over two-thirds of percid species belong to the Etheostomatinae, with the greater part of those in the genus Etheostoma (which, however, may not be monophyletic).

*Though the non-monophyly of Percinae found by Sloss et al. is in contrast to their breeding behaviour - Percinae differ from other percids in laying their eggs encased in long gelatinous strands, while Luciopercinae and (ancestrally) Etheostomatinae are broadcast spawners.

The European perch, Perca fluviatilis. A very similar species, Perca flavescens, is found in North America. Photo from here.

Human interest in the Percidae (as with most matters, really) has usually been related to one of two things - eating or sex. The larger percids of the "Percinae" and Luciopercinae are widely caught for food, and the European perch Perca fluviatilis has been introduced to many localities outside its native range such as New Zealand for the amusement of anglers. Some percids, such as the walleye Sander vitreus, have been recorded reaching lengths of over a metre (though such sizes are, of course, exceptional - a more average walleye would be about twenty centimetres). Species of the Etheostomatinae, known as darters, are not targets of fishing - members of this subfamily (as well as some species of Luciopercinae) are smaller than other percids, less than ten centimetres in length*, and wouldn't offer much in the way of eating. Still, darters more than make up their interest in the other regard of sex. They show a wide diversity of breeding behaviour, from broadcast spawners to some that bury their eggs in sediment or gravel to species that lay their eggs safely hidden on the underside of rocks. Other species may glue their eggs to vegetation (Winn, 1958a, b). During the breeding season, most (but not all) darters move from deeper to shallower waters (many species favour riffle areas) where the males usually establish a breeding territory (as reported by Winn, 1958b, the presence of other males seems to be required to incite the successful establishment of a territory - solitary males tended to lose interest in a potential territory and wander off). Some darter species are fairly relaxed about their territories and only fend off males of their own species, but other darters may be decidedly pugnacious and attack just about anything that moves. Challenging males approach each other with fins held high, and their colours will often become brighter. They may circle each other and butt or bite at each other's tail regions. After a male has mated with a female and she has laid her eggs, he may or may not remain in the area to guard them. Experiments have shown that if the eggs are removed or replaced, the male continues to guard the same spot, so it is the territory that induces guarding behaviour rather than the presence of eggs. Hybrids have been recorded between a number of darter species and seem to be not uncommon, especially where species have been spread outside their native range (Stauffer et al., 1995).

*As a corollary of their smaller size, it is worth noting that darters (and the smaller Luciopercinae) also lack swim bladders.

Percarina demidoffi as illustrated by N. Kondakov in a 1957 Russian textbook. For some reason, I find a certain whimsy in this illustration of what is perhaps one of the more mysterious percids. Image via NOAA Photo Library.

REFERENCES

Reeves, C. D. 1907. The breeding habits of the rainbow darter (Etheostoma cœruleum Storer), a study in sexual selection. Biological Bulletin 14 (1): 35-59.

Sloss, B. L., N. Billington & B. M. Burr. 2004. A molecular phylogeny of the Percidae (Teleostei, Perciformes) based on mitochondrial DNA sequence. Molecular Phylogenetics and Evolution 32 (2): 545-562.

Stauffer, J. R., Jr, J. M. Boltz & L. R. White. 1995. The fishes of West Virginia. Proceedings of the Academy of Natural Sciences of Philadelphia 146: 1-389.

Winn, H. E. 1958a. Observation on the reproductive babits of darters (Pisces-Percidae). American Midland Naturalist 59 (1): 190-212.

Winn, H. E. 1958b. Comparative reproductive behavior and ecology of fourteen species of darters (Pisces-
Percidae). Ecological Monographs 28 (2): 155-191.

(Belated) Taxon of the Week: The Bishop's Mitra

noreply@blogger.com (Christopher Taylor) — Fri, 26 Jun 2009 03:58:00 +0000

Mitra cardinalis. Photo from Sydney Shell Club.

The marine gastropods of the genus Mitra get their genus name (as well as their common name of 'mitre shells') from the resemblance of many species, at certain angles, to the pointy hat of a bishop (and indeed, the species names Mitra episcopalis, M. pontificalis and M. papalis all appear to be floating around out there). They are fairly middling-sized shells - three or four centimetres long would seem to be a respectable Mitra size - and most of them are slender and pointed at one end (the technical term is 'fusiform', and the discription 'cigar-shaped' gets bandied about regularly). Members of the subgenus Strigatella, however, are shorter, more globular animals.

Mitra are members of the family Mitridae, which is in term a family of the Neogastropoda. Neogastropods have been featured at this site before (here and here), albeit without having been identified as such, and there is a fair probability that if you go looking for gastropods on a trip to the beach that the first one you find will be a neogastropod. This is not so much because neogastropods are that much more abundant than other marine gastropods (although they are a fairly speciose bunch) as because neogastropods tend to be a lot more active than other gastropods, and are much more likely to be visibly on the move while other gastropods are sitting clamped to rocks. And the reason for the greater mobility of neogastropods is a matter of diet.

Mitra idae. Note the siphon protruding in front of the shell. Photo from Wikipedia.

The ancestral diet for gastropods was a reliable, if somewhat unexciting, scraped meal - algae rasped off rocks, or the fruits of scavenging. As a result, mobility is not at much of a premium for most gastropods - it doesn't take much speed to chase down a patch of algae - and the only reason to move is to get to the next patch of algae. Neogastropods, however, tired of this diet and went for something a little more exiting - they became active predators. Mobile neogastropods at the beach are on the hunt for prey (or, alternatively, pre-deceased animals to scavenge off). One of the most distinctive features of neogastropods to the casual observer is their elongate siphon, which in live animals can usually be seen extended from the front of the shell (which has a distinct notch or anterior extension for it to extend through), waving back and forth as the animal moves, sniffing for any appetising scents. The radula (the tongue-like structure covered with teeth in the mouth of a gastropod) has become adapted to the predatory life-style, with the number of teeth reduced but each individual tooth much larger and sharper. The fusiform body-shape as seen in most Mitra also appears well-suited to mobility, and is shared by a significant proportion of neogastropods.

Mitra mitra everting its proboscis. Photo from here, where they've made the mistake of thinking this individual is swallowing a worm.

Members of the family Mitridae possess a particularly elongate proboscis, often longer than the rest of the animal. Running along the inside of the proboscis is the radula and a muscular rod called the epiproboscis, which can be even further extended. Mitrids are specialist feeders on sipunculan worms, which live buried in sediment or burrowed into corals (Taylor, 1989), and the epiproboscis is used to capture their prey. Suggestions that it is used to inject digestive enzymes into the prey for external digestion are incorrect, as the prey is usually swallowed directly without allowing time for digestion (Taylor, 1989) The method used by Mitra idae to capture a sipunculan was described by West (1990), and as the morphology of the epiproboscis is fairly constant within the Mitridae other species probably use the same or a very similar method. After locating a sipunculan with its siphon, the gastropod would extend its proboscis until it contacted the worm, then the epiproboscis to grab onto the worm. The first move of the Mitra would then be to try and suck the worm directly out of its burrow. If this failed (which I suspect would be the norm), it would then use its radula to rasp a hole through the worm's skin before inserting the epiproboscis through the hole. The epiproboscis would entwine itself around the worm's viscera and grab directly onto its intestines. The viscera would then be hauled out through the hole in the sipunculan's skin and slurped down the waiting proboscis. Once the Mitra had pulled as much of the worm's guts out as it could, it would close its proboscis over the remaining husk and finish drawing the worm out from its hole. Insertion and retraction of the epiproboscis took a little under ten seconds. The whole process, from initial insertion to final withdrawal, could take up to twenty minutes.

REFERENCES

Taylor, J. D. 1989. The diet of coral-reef Mitridae (Gastropoda) from Guam; with a review of other species of the family. Journal of Natural History 23: 261-278.

West, T. L. 1990. Feeding behavior and functional morphology of the epiproboscis of Mitra idae (Mollusca: Gastropoda; Mitridae). Bulletin of Marine Science 46 93): 761-779.

Keeping an Eye on Inflation

noreply@blogger.com (Christopher Taylor) — Mon, 22 Jun 2009 02:14:00 +0000

Neofelis diardi, the "new" clouded leopard species (actually first described in 1823, but later sunk into synonymy until recently resurrected) that has become something of a poster child for arguments on the worth of recent vertebrate species splits. Photo from Tet Zoo.

Normally, there'd be a Taxon of the Week post here on a Monday, but due to various circumstances that won't be happening today. Instead, here's something I've been sitting on for a few days now:

Sangster, G. (in press) Increasing numbers of bird species result from taxonomic progress, not taxonomic inflation. Proceedings of the Royal Society of London Series B.

Despite the widespread (and, I should note, entirely valid) complaints about the decline of taxonomy as a field of research, a person unfamiliar with the dynamics of the field might possibly be forgiven if, on a cursory glance, they saw it as stronger than ever. The number of new taxa, particularly species, being described every day has not appreciably slowed down - indeed, new species are probably debuting faster than ever. In many cases, study of a "species" once believed widespread has lead to the recognition of multiple species, each occupying a different part of the originally-recognised taxon's "range". This latter pattern is particularly noticeable in studies on vertebrates. Often, the new "species" were previously recognised as "subspecies" before their promotion. This has led to the accusation that such cases are examples of taxonomic inflation.

Lesser bird of paradise, Paradisaea minor. Birds of paradise have become one of the prime examples of conflict between the Biological and Phylogenetic Species Concepts. Most authors claiming to follow the BSC have recognised about forty species of bird of paradise (and that total is possibly oversplit, considering the high interfertility of the recognised species), but applications of the PSC to the family have suggested more than ninety species. Photo by stboed.

For those of you unfamiliar with the term, the term "taxonomic inflation" refers to situations where names, but not the content, of taxa change as a result of their elevation in rank. When the term is used, it usually carries the disparaging implication that this is change simply for the sake of change without any underlying gain in information, and hence unnecessary at best and a misleading waste of everyone's time at worst*. Taxonomic inflation has also been cited as a problem with the use of the Phylogenetic Species Concept (PSC) rather than the Biological Species Concept (BSC) (see here for an earlier post of mine on the subject). Many authors have complained that the rise in recognised species is bad news for conservation, as it increases the number of required conservation targets.

*Personally, I (and others before me) would argue that taxonomic inflation is an inevitable side-effect of our current use of a rank-based classification. As I complained last week, an unfortunate side-effect of the pinning of our ranking system on certain primary ranks leads to the belief (whether concious or subconcious) that those ranks should be used for the most "significant" taxa. Now, imagine that I'm a researcher spending five years working on a particular family of organisms. As a result of my research, I find that my "family" of interest renders another "family" paraphyletic. Assuming that I prefer a classification recognising all-monophyletic taxa, I have two options - either I can subsume my "family" of interest into the other family, or I can divide up the other "family" in order to maintain the distinctiveness of my research family. It all depends on my perception of the relative significance of the taxa - and what do you think that might be, considering into what I've been investing the last five years of my life?

Variation in appearance between different populations of giraffe, Giraffa spp. Usually recognised as a single species, G. camelopardalis, recent authors have suggested giraffes should be divided between a number of species. Image from The Barcode Blog.

The new paper by Sangster responds to the claim that the increase in recognised vertebrate species is due solely to the increased popularity of the PSC, and does not reflect any net increase in our taxonomic understanding (invertebrate taxonomy has been less affected by this debate, because invertebrate systematists have, for the most part, been less inclined to recognise "subspecies" [with the notable exception of lepidopterists]). According to Sangster, if this claim is true, it leads to four predictions: (1) the increase in recognised species would have not begun until the introduction of the PSC in the early 1980s*; (2) most taxonomic changes would be based on reinterpretations of old data rather than on collection of new data; (3) most taxonomic splits would be based on specifically PSC-related criteria such as diagnosability and reciprocal monophyly to each other and other taxa, as opposed to less specifically PSC-related criteria such as degree of difference ("too different" to be the same species, or "too similar" to be different species), differences in adaptive zone (e.g. lowland vs montane taxa) or reproductive isolation; and (4) new taxonomic splits would be biased towards members of charismatic groups (in which there may be more of a vested interest in raising their conservation profile). To test these predictions, Sangster surveyed taxonomic proposals affecting taxon rank published in seven major ornithological journals (such as The Auk and Ibis) between 1950 and 2007 - whether proposals recommended a split (subspecies becoming species) or lump (species becoming subspecies), and what were the criteria cited as support for the proposal.

*The date is inexact because a number of variants on the PSC were proposed by different authors.

The results of Sangster's survey showed that the increase in the percentage of taxonomic proposals recommending splits rather than lumps (shown in the graph above from the paper) had been continuous over the time period surveyed, and the rate of increase had not significantly changed in the 1980s (indeed, there had been a slight downturn in the 2000s, though probably not a significant one). 76.4% of taxonomic proposals over the period covered had been supported by new data rather than based on reinterpretation of old data, and proposals for splits were significantly more likely to be based on new data than proposals for lumps (84.6% vs 64.2%). Prior to the introduction of the PSC, 71.7% of proposed splits were based on new data - post-PSC, 93.9% of them were. Only 10.3% of proposed splits overall were based solely on reinterpretation of old data using PSC-related criteria.

The most common criterion for a proposal was diagnosability, followed by reproductive isolation. The least commonly used criteria related to reciprocal monophyly. All criteria were more likely to lead to splits than lumps, though "degree of difference" had the smallest difference in propensity. Proposals based only on PSC-related criteria were more likely to lead to a split than those based only on non-PSC criteria, with the latter more likely to propose a lump than a split. There was no correlation between the increase of species in a family and the charisma of that family, but there was a correlation between the number of splits and the number of polytypic species (i.e. species divided into subspecies) in that family.

The two storm petrel species breeding on the Azores, of which Oceanodroma monteiroi was only described last year in Bolton et al. (2008), from which comes this figure. Though very similar, the two species breed at different times of the year.

Sangster concludes that the accusation that recent increases in species number are based solely on reinterpretation of old data is grossly unfounded. Proposed changes aren't taxonomic "inflation", they're taxonomic "progress". However, as much as I personally like his conclusion, it must be admitted that Sangster is potentially setting up a strawman here. Taxonomic research does not exist in a vacuum, and an author is not very likely to go about revising the taxonomy of a group unless they are working on that group already. The increase in the proportion of taxonomic changes supported by new data might indeed reflect changes in researcher practice - or it may reflect the journals becoming more discerning about what manuscripts they will accept for publication (still, for the reader it may not really matter whether the increased rigour is being driven by the researcher or the publisher).

On the other hand, Sangster brings up the very important point that many of these "new" species aren't really new at all. During the early 1900s, vertebrate taxonomy went through a period of significant lumping. Sangster cites the point that while Sharpe recognised 18,939 species of bird in 1909, Mayr & Amadon recognised only 8590 in 1951 - less than half Sharpe's total. The justification for this lumping was often unclear (they were in a time period when a researcher's authority was generally taken for granted, rather than their being required to show their working), and many current taxonomists feel that in many cases the lumping went too far (for a concrete example, see Darren Naish's post from a few years back on babirusas). Many proposed splits are arguably correcting the excesses of the past.

Finally, on a personal level, I wouldn't particularly care even if the species increase was based on a change in species concept, because as I've explained before (see the first post linked to at the top of this one), I'm a much greater fan of the PSC than of the impractical-to-test, everyone-says-they-follow-it-but-pretty-much-no-one-actually-does mess that is the Biological Species Concept. The conservation and PR argument cited above - that the PSC somehow leads to there being "too many" species - completely fails to impress me, because I don't think that scientific investigation should be directly influenced by political concerns. Once you have the information, then you can work out what to do about it, but changing your working information to what you want it to be first is just not on.

42

noreply@blogger.com (Christopher Taylor) — Thu, 18 Jun 2009 03:18:00 +0000

Here are the answers to yesterday's quiz:

1. Current rank-based taxonomy is based on seven primary ranks. Which two were not used by Linnaeus?

Okay, that was an easy one to start off with. Linnaeus didn't use "families" or "phyla" (and for animals, he only recognised six "classes" - mammals, birds, amphibians [including reptiles], fish, insects [including other arthropods] and "worms" [pretty much anything soft and squishy, and not necessarily even worm-like]).

2. What are the five codes of biological nomenclature currently in action?

Mike Keesey even had the titles - International Code of Zoological Nomenclature, International Code of Botanical Nomenclature, International Code of Nomenclature of Bacteria (now the International Code of Nomenclature of Prokaryotes, in light of the increasing tendency not to refer to archaebacteria as 'Bacteria'), International Code of Virus Classification and Nomenclature, and International Code of Nomenclature of Cultivated Plants. The last one, if you were wondering, covers the registration of names for varieties bred in horticulture, such as a cauliflower Brassica oleracea 'Snow Ball'.

3. Name one group of organisms not governed by any of these five codes.

Since the bacterial code went its separate way from the botanical code, fossil prokaryotes have been left effectively homeless. The botanical code no longer regulates prokaryotes except for Cyanobacteria (so those fossil prokaryotes identified as cyanobacteria would still be regulated), while the bacterial code is effectively inapplicable to non-living taxa (it requires deposition of a sample of the living type strain in at least two collections in two different countries for a taxon to be valid). Mike's guess that stem-biotes were the organisms in question is therefore partially correct, because it is possible (albeit probably not ever demonstrable) that a fossil prokaryote could be a stem-biote.

4. What is the earliest publication using binomial nomenclature to be currently recognised by the ICZN?

This was meant to be a trick question, but sadly no-one fell for the trick. While the 10th edition of Linnaeus' Systema Naturae, published in 1758, is the official starting point for binomial nomenclature under the ICZN, Andreas Johansson correctly pointed out that one earlier publication, Clerck's 1757 Svenska Spindlar uti sina hufvud-slågter indelte samt under några och sextio särskildte arter beskrefne och med illuminerade figurer uplyste - Aranei Svecici, descriptionibus et figuris æneis illustrati, ad genera subalterna redacti, speciebus ultra LX determinati (usually referred to simply as Aranei Svecici, for obvious reasons), has been accepted by the ICZN as admissible (and officially takes priority over Linnaeus). You can read the entirety of Aranei Svecici online through this site.

5. When and what was the earliest formal zoological nomenclatural code proposed? What was the earliest botanical code?

Mike did refer to the 1842 Strickland Code, but unfortunately for Mike the object of the Strickland Code was zoology, not botany. As I previously alluded to at the beginning of an earlier post, botanists at the time rejected the idea of extending the Strickland code to cover their territory (the open-access article linked to at that post also transcribes a large part of the Strickland Code, for anyone interested in reading it). The first Botanical code to be formally adopted was the Lois de la Nomenclature Botanique published by Alphonse de Candolle in 1867. Ironically, while the zoologists had a twenty-five-year head-start over the botanists in establishing a code, it was the botanists that actually paid attention to theirs, while the Strickland Code ending up largely falling by the wayside. As such, botanical nomenclature ended up becoming a lot more stabilised a lot earlier than zoological nomenclature.

6. What do the letters 'VP' and 'AL' mean as part of a bacterial name?

Originally, bacteria were dealt with using the Botanical Code, but as time went by it became increasingly clear that the provisions of that code were not suitable for working with prokaryotes (which are mostly distinguished by chemical rather than physical characteristics), with thousands of excess names for bacterial taxa having been proposed for which no-one had the slightest idea to what they referred, and eventually a separate Bacterial Code was established. Those bacterial taxa that had been well-characterised were listed in the Approved Lists of Bacterial Names, published in 1980, and any taxa from before 1980 that were not on the Approved Lists were effectively null or void. Any bacterial name published after 1980, in order to be valid, had to be either published or validated in the International Journal of Systematic Bacteriology (now the International Journal of Systematic and Evolutionary Microbiology). To indicate the mode of validation, the full citation for a bacterial name will have the letters 'AL' or 'VP' as a superscript against the publication date - 'AL' indicates a name was on the Approved Lists (in which case it takes priority from the original date of publication), while 'VP' (for 'Valid Publication') indicates that it was validated by publication in the IJSEM (in which case it is dated from it appeared in that journal, no matter how much earlier the name may have appeared elsewhere).

7. Kathablepharis and Katablepharis are different spellings for the name of the same organism. Each is the one spelling that must be used, while the other spelling is invalid. Explain.

Mike was halfway there with this one - Katablepharis is a protist that has been treated by different authors using both the zoological and botanical codes. Its name was originally published as Kathablepharis by Skuja in 1939, but the correct Latinisation should have been Katablepharis. In such cases, the botanical code requires that the name be corrected, but the zoological code requires that the original spelling be maintained. Hence the correct name of this organism ended up being spelt differently depending on which code it was being treated under.

8. The name Oedicnemidae was published by Gray in 1840. The name Burhinidae was published by Mathews in 1912. Both refer to the same family, for which the valid name is Burhinidae. Why?

Okay, take a deep breath. This one gets a little involved, but the situation it refers to is actually not that uncommon. Genus- and species-level nomenclature can be confusing enough, but sometimes family-level nomenclature is just plain evil.

It used to be the tradition that when the type genus of an animal family was synonymised with another genus, the name of the family also changed to match. So when Oedicnemus was synonymised with Burhinus, Oedicnemidae became known as Burhinidae. Where this gets confusing is that the altered name continued to take its priority from the original name - so the name Burhinidae would be treated as dating from 1840, when Oedicnemidae was published, even though the name Burhinidae itself never actually existed until 1912. When the modern Zoological Code was first published in 1961 (well, before that, even), it was realised that this was far too complicated and confusing a way to do things (especially in cases of debated synonymy), and so the current rule was introduced that family names were determined only by their own priority, and the synonymy of its type genus did not affect the validity of a family name. However, because the ICZN does not mess with past actions when introducing new rules, if a family name was changed under the old tradition before 1960, it retained the new name. So the then-current name Burhinidae stayed Burhinidae, and didn't have to revert to the probably long-forgotten name Oedicnemidae.

9. If two or more taxa have the same name, and fall under the scope of the same code, then their names are homonyms, and only one can be valid. Pupa affinis Rossmaessler 1839, Pupa affinis Aradas & Maggione 1843 and Pupa affinis (Adams 1855) are all names for animals, but they are not considered homonyms. How is this possible?

Mike got this one right off the bat. The three names are not counted as homonyms because they are not actually in the same genus - they are in three different genera that had each been named Pupa. The genus names have to be corrected because they are homonyms, but the species that were published in association with those genera can keep their original names.

Picture credits (from top to bottom): Dante being examined on theology in heaven, from Il Paradiso, via here.

The Beaver's Lesson, from The Hunting of the Snark.

Examition of a Witch, by T. H. Matteson, via here.

"Lojban" from xkcd.

Satan in Heaven, from Paradise Lost, via here.

Completely Frivolous Taxonomy Quiz

noreply@blogger.com (Christopher Taylor) — Wed, 17 Jun 2009 02:36:00 +0000

For no good reason, here's a set of trivia questions about biological taxonomy and nomenclature. Excuse the possible zoological bias - I am a zoologist, after all. How many can you answer? They start off easy, but (hopefully) they get trickier.

1. Current rank-based taxonomy is based on seven primary ranks. Which two were not used by Linnaeus?

2. What are the five codes of biological nomenclature currently in action?

3. Name one group of organisms not governed by any of these five codes.

4. What is the earliest publication using binomial nomenclature to be currently recognised by the ICZN?

5. When and what was the earliest formal zoological nomenclatural code proposed? What was the earliest botanical code?

6. What do the letters 'VP' and 'AL' mean as part of a bacterial name?

7. Kathablepharis and Katablepharis are different spellings for the name of the same organism. Each is the one spelling that must be used, while the other spelling is invalid. Explain.

8. The name Oedicnemidae was published by Gray in 1840. The name Burhinidae was published by Mathews in 1912. Both refer to the same family, for which the valid name is Burhinidae. Why?

9. If two or more taxa have the same name, and fall under the scope of the same code, then their names are homonyms, and only one can be valid. Pupa affinis Rossmaessler 1839, Pupa affinis Aradas & Maggione 1843 and Pupa affinis (Adams 1855) are all names for animals, but they are not considered homonyms. How is this possible?

Picture credits (from top to bottom): Tweedle Dum from Alice Through the Looking Glass, via here.

Satan in Hell from L'Inferno, via here.

The Ship of Fools by Hieronymus Bosch, via here.

Hey, Old Taxo! My Genus is Better than Yours!

noreply@blogger.com (Christopher Taylor) — Tue, 16 Jun 2009 03:38:00 +0000

In the children's picture book The Kuia and the Spider by New Zealand author Patricia Grace, an elderly woman (kuia in Maori) is challenged by a spider living in her kitchen, who keeps saying to her, "Hey, old woman! My weaving/cooking/etc. is better than yours!" Each successive challenge leads to frantic competition, as the woman and the spider try to outdo each other ("cooking" for the spider, of course, refers to the process of catching, wrapping and breaking down flies). However, each of these competitions ends in an effective draw - they only way they could end, because neither competitor is willing to admit the other's superiority in these ultimately subjective comparisons.

As my regular readers will probably be aware, I'm not a big fan of rank-based classifications (see here for one of my earlier rants on the subject. The ultimate problem with rank-based taxonomy is that the urge to inject some sort of "reality" into the concept of ranks is irresistible. Defenders of the rank system claim that this is not a problem - ranks only indicate relative positions, and it does not matter that a "genus" of insects is not directly comparable to a "genus" of mammals, because that's not the point of ranks. Unfortunately, they then forget this point themselves - instantaneously, even:

Everyone accepts that Linnaean ranks are subjective, and yet there is no benefit in abandoning ranks because they have proved to be of such value to users of classifications, and genera and families, for example, act as valuable surrogates for species in large−scale evolutionary and ecological studies. (Benton, 2007)

If ranks are subjective (as supposedly everyone says they are), then higher ranks cannot possibly act as surrogates for species for the simple reason that one author's rank-ometer may be (and, in practice, usually is) calibrated differently from another author's.

The point I really wanted to make today, though, is another aspect of the fallacy of thinking of ranks as "real". The current taxonomic ranking system, as we all know, is anchored on the principle that Kind People Can Often Find Good Sex. The seven ranks referred to by that mnemonic are the primary and more or less mandatory ranks of the system, while all other more optional ranks are conceptualised in their relationship to the primary seven. Unfortunately, this leads directly to the idea that taxa at those "primary" ranks are somehow more significant than taxa at the "subsidiary" ranks. Take this comment made recently on the Taxacom mailing list:

Ideological extinction is the fate of autophyletic (descendant groups recognized at same taxonomic level as ancestor) taxa, and of paraphyletic taxa split into non-recognition. Although taxa of high visibility (Aves, polar bears) seem immune to ideological extinction, many groups simply disappear from classification because they were embedded in an ancestral group of the same rank. In my own field, bryology, three families (Ephemeraceae, Cinclidotaceae, and Splachnobryaceae) have been sunk in a recent influential phylogenetic classification into one larger one (Pottiaceae) without discussion because they were autophyletic in previously published molecular trees; their names do not appear anywhere in the classification, which offers no synonymy.

The author of the comment, Richard Zander, is complaining that the subsumation of the three smaller families into the larger family obscures the distinctiveness of the three smaller groups. There is no particular reason why this should be so - if the taxa originally labelled by those three names are still good taxa, then they should still be perfectly recognisable whatever rank they are put at. The only reason why it should make a difference that they have lost their status as separate families is if there is some particular significance to being a "family" as opposed to a subfamily, tribe or whatever. If ranks are truly only relative, and there's no real significance to them, then why are you complaining?

REFERENCES

Benton, M. J. 2007. The PhyloCode: beating a dead horse? Acta Palaeontologica Polonica 52 (3): 651-655. (Thank you to David Marjanović for pointing this out to me.)

Multifarities Most Horrid (Taxon of the Week: Braconidae)

noreply@blogger.com (Christopher Taylor) — Mon, 15 Jun 2009 03:50:00 +0000

Braconid wasp of the subfamily Aphidiinae laying an egg in a hapless aphid. Photo from BioMed Central.

We all know that J. B. S. Haldane is supposed to have remarked that God seemed to have an "extraordinary fondness for beetles". What Haldane may not have realised was the possibility that the beetles were just a means to an end. As the current rate of taxonomic description is considered, some researchers have come to the suspicion that the true objects of the Creator's affection are not beetles, but parasitoid wasps*. Which, when you consider the natures of parasitoid wasps, kind of explains some things about life.

*Personally, I'm still taking the long odds and backing the nematodes.

Microgastrinae larvae emerging from a host caterpillar. Photo from here.

The Braconidae are just one of the stupidly diverse lineages of Hymenoptera (another group, the Proctotrupomorpha, was covered at this site here). According to ToLWeb (in 2004), there are some 12,000 described species of braconids, with estimates of up to 50,000 in total. Braconids form the living sister group to the similarly diverse Ichneumonidae, though braconids tend to be smaller in size (still, some of them are more than big enough). Braconids include both exoparasitic and endoparasitic taxa, parasitoids of eggs, larvae or adult insects, and a small number of gall-forming plant-parasitic taxa for added variety. The usual opinion is that the exoparasitic taxa represent the ancestral lifestyle for the family, but the actual phylogeny of the family is still being hammered out (and the "usual opinion" may yet turn out to be the wrong opinion). About forty subfamilies are currently recognised, but most authors (e.g. Shi et al., 2005) divide those subfamilies between three main lineages, the cyclostomes, microgastroids and helcionoids, with some subfamilies of uncertain position relative to the three. The microgastroids and helcionoids are all koinobiont endoparasitoids (after the wasp has laid its eggs in the host, the host continues to grow and develop), while the cyclostomes include both exoparasitoids and endoparasitoids, with exoparasitoids usually paralysing the host before laying their eggs (Wharton, 1993). The microgastroids are fastidious in their tastes, restricting their diet to Lepidoptera (Murphy et al., 2008), while helcionoids attack a wide variety of hosts, including hemimetabolous as well as holometabolous insects. Early phylogenetic studies suggested that the cyclostomes (which possess a distinctive mouthpart morphology) were paraphyletic with regard to the other braconids, but more recent studies support a monophyletic cyclostome clade (Shi et al., 2005). The monophyly of a microgastroid + helcionoid clade is supported by molecular data (Shi et al., 2005), but remains short on morphological support (Quicke et al., 1999).

An individual of the genus Atanycolus (subfamily Braconinae in the cyclostome group). Photo by Richard Bartz.

The Aphidiinae are the largest group of braconids to not fit comfortably within the three-way division. Aphidiinae are parasitoids of aphids. Morphological data supports a relationship between aphidiines and the cyclostome group (Quicke et al., 1999), but the molecular analysis of Shi et al. (2005) suggested a relationship between the Aphidiinae and the Euphorinae, members of the helcionoids. The intriguing feature of this result is that Aphidiinae and Euphorinae both have the unusual characteristic (for insect parasitoids) of parasitising adult hosts rather than larvae - albeit with different host ranges in the two subfamilies. Euphorinae were probably originally parasitoids of beetles, but some species have since become parasitoids of hosts as diverse as grasshoppers or Psocoptera. (A more recent combined morphological and molecular study whose authors argued against an Aphidiinae-Euphorinae relationship in favour of an Aphidiinae-cyclostome connection [Zaldivar-Riverón et al., 2006] actually did not test anything either way, because the authors' choice of taxa and outgroup effectively forced an a priori cyclostome position).

An adult of Microgastrinae. Photo by Scott Justis.

Finally, some would think it rather remiss of me to write about braconids without making some mention of polydnaviruses, but I don't see why I should when a much better description of such things than I could produce has already been written by Merry Youle at Small Things Considered. After you read the main article there, though, make sure you scroll down the comments to Merry's description of the differences between polydnaviruses in Braconidae and Ichneumonidae suggesting the independent origins of the polydnavirus system in the two families. As well as the differences described by Mary, it also turns out that polydnaviruses are not characteristic of braconids as a whole, but are in fact only found within the microgastroid clade (Wharton, 1993), so an independent origin from ichneumonid polydnaviruses has phylogenetic as well as biochemical support.

REFERENCES

Murphy, N., J. C. Banks, J. B. Whitfield & A. D. Austin. 2008. Phylogeny of the parasitic microgastroid subfamilies (Hymenoptera: Braconidae) based on sequence data from seven genes, with an improved time estimate of the origin of the lineage. Molecular Phylogenetics and Evolution 47 (1): 378-395.

Quicke, D. L. J., H. H. Basibuyuk & A. P. Rasnitsyn. 1999. Morphological, palaeontological and molecular aspects of ichneumonoid phylogeny (Hymenoptera, Insecta). Zoologica Scripta 28 (1-2): 175-202.

Shi, M., X. X. Chen & C. van Achterberg. 2005. Phylogenetic relationships among the Braconidae (Hymenoptera: Ichneumonoidea) inferred from partial 16S rDNA, 28S rDNA D2, 18S rDNA gene sequences and morphological characters. Molecular Phylogenetics and Evolution 37 (1): 104-116.

Wharton, R. A. 1993. Bionomics of the Braconidae. Annual Review of Entomology 38: 121-143.

Zaldivar-Riverón, A., M. Mori & D. L. J. Quicke. 2006. Systematics of the cyclostome subfamilies of braconid parasitic wasps (Hymenoptera: Ichneumonoidea): a simultaneous molecular and morphological Bayesian approach. Molecular Phylogenetics and Evolution 38 (1): 130-145.

Remarkable Things

noreply@blogger.com (Christopher Taylor) — Thu, 11 Jun 2009 03:47:00 +0000

Yesterday was indeed a day for remarkable things. It started when I walked into the bathroom this morning and found a winged male embiopteran sitting on the wall above the toilet cistern. Not the usual place where one would expect to find an embiopteran. It continued when I was informed of the publication of not one but two papers of note on harvestmen.

Lateral view of the male of Neopantopsalis thaumatopoios with most of the legs removed (because there's a limit to how much I'm willing to draw). Even for harvestmen, species of Neopantopsalis have stupidly long appendages. This figure was used in Taylor & Hunt (2009). The scale bar equals a millimetre.

The first is of note on a more personal level - my paper on the new genus Neopantopsalis has come out in Zootaxa (Taylor & Hunt, 2009). This is the first of the three major papers that will be coming out of my PhD - the other two (which I'm still in the process of writing) will cover the genera Megalopsalis and Spinicrus, respectively, as well as the phylogeny of the family Monoscutidae as a whole (or, at least, as much of it as I can reliably make out - long-legged harvestmen aren't exactly brimming over with phylogenetically useful characters). But now that the Neopantopsalis paper has completed the review process and made it into print, I can safely say that I'm not entirely happy with it. I began working on it when I found that Glenn Hunt, the last major worker on Australian harvestmen, had designated a specimen in the Queensland Museum as the type of a new species that he had unfortunately never published before he passed away (in recognition of this, I included Glenn as a second author on my manuscript). This species, it turned out, was one of a well-defined group of species found in Queensland and northern New South Wales - the group now labelled by the name Neopantopsalis. Unfortunately, distinguishing individual species within Neopantopsalis threatened to become an overwhelming task. Individual variation in almost every character was the norm rather than the exception, and in more than one case I was left at a loss to decipher whether I was dealing with a species complex or a complex species. Eventually realising that I could end up spending my entire doctorate working on this one genus (which would not be ideal), I was forced to cut my losses, pick out some well-defined exemplars that could stand in for the overall diversity, and put an appropriate manuscript together as best I could so I could move on to the next topic. So if anyone with a penchant for arachnid systematics with connections to the Queensland region is ever looking for something to do, there's a very widespread genus there still begging to be given the attention it really requires.

The fossil remains of Mesobunus martensi, the better-preserved of the two recent finds. Figure from Huang et al. (in press).

The other paper I learnt of yesterday has perhaps got a broader appeal - the first Jurassic harvestman fossils (Huang, Selden & Dunlop, in press, 2009). Harvestmen are purely terrestrial, not particularly vagile and mostly very delicately built. As a result, their fossil record can only be described as pitiful. There's a couple of fossils from the Devonian, a small collection from the Carboniferous, a couple from the Cretaceous and a small smattering from the Cenozoic (mostly amber) (Dunlop, 2007). However, the few fossils that we do have are quite remarkable in light of how incredibly unremarkable they are. Most fossil harvestmen are almost indistinguishable from taxa living today. Even the very oldest known harvestman, Eophalangium sheari from the Rhynie Chert, would probably fail to raise a single eyebrow if reanimated and released into the modern environent. The origin of harvestmen could not have been all that long before the time of Rhynie Chert, because it wasn't that long before then that there wasn't even a terrestrial environment for there to be harvestmen in. Harvestmen, it seems, are the ultimate retroactive conservatives - if it was good enough 400 million years ago, it's good enough today.

The two new Jurassic fossils, coming from Daohuguo in China, do not buck this trend in the least. Indeed, so similar to modern long-legged harvestmen are they that Huang et al. even assign the better-preserved of the two, Mesobunus martensi, to the modern family Sclerosomatidae (this is the family that includes the genera Gagrella and Leiobunum). They do this on the basis of "the extremely elongate legs, a single tarsal apotele [claw], a pediform [leg-like] pedipalp, and, particularly, the fusion of the first five opisthosomal tergites into a single dorsal plate". They also note the presence of what may (or may not) be pseudoarticulations in femora of the fourth pair of legs, which (if present) would not only place Mesobunus in the Sclerosomatidae, but also within the subfamily Gagrellinae within the Sclerosomatidae. The long legs, simple claw and leg-like pedipalps are plesiomorphies for the harvestman superfamily Phalangioidea (and quite possibly for a larger subgroup of harvestmen), so are not really significant. The dorsal scute and possible pseudoarticulations are more interesting - but, unfortunately, not conclusive. A similar dorsal scute is found in other harvestmen in other suborders (such as the genus Ischyropsalis), and also (though less sclerotised) in some members of the eupnoan family Monoscutidae (notably the genus *ahem*, which however doesn't have very long legs*). Femoral pseudoarticulations are also not unique to Sclerosomatidae - for instance, they have recently been recorded in two species of Monoscutidae by - oh, will you look at that - Taylor & Hunt (2009). So while it is true that Sclerosomatidae is the only living family that shows the exact combination of characters seen in Mesobunus, none of the characters individually is unique. Or to turn that around, while I'm not entirely convinced that Mesobunus is a sclerosomatid, I can't exactly show that it's not a sclerosomatid either. Unfortunately, a rock-solid identification with Sclerosomatidae would probably require examination of features such as the genitalia or spiracles - both highly unlikely to be visible in a fossil.

*I say "ahem" because it's in press as we speak.

Reconstructions of Mesobunus from Huang et al. (in press).

If we accept for the present that Mesobunus is a sclerosomatid, that has some interesting implications for harvestman biogeography. The Phalangioidea can be roughly divided into two morphological groups, a mostly Northern Hemisphere group containing the families Phalangiidae and Sclerosomatidae, and a Southern Hemisphere group containing the families Neopilionidae and Monoscutidae*. The Phalangiidae + Sclerosomatidae group is well supported by a few good characters (most notably the structure of the spiracle) and is more than likely a good clade. The characters uniting the Southern Hemisphere families, on the other hand, are probably plesiomorphies, so this group is quite possibly paraphyletic with regard to the Northern clade (though exact relationships are currently unknown). Similar patterns, with Northern Hemisphere taxa nested among Southern Hemisphere taxa, have been observed in many groups of organisms, and it has often been suggested to indicate a Gondwanan ancestry for those groups. Birds, butterflies... there was a period when it seemed almost everything came from Gondwana. Usually, such Gondwanan ancestries were suggested to be related to the mass extinction at the end of the Cretaceous - with the Northern Hemisphere more heavily affected by the end-Cretaceous meteor impact than the South (which is entirely plausible if the Chicxulub crater in Mexico is the site of the impact), Southern Hemisphere taxa were able to radiate at the beginning of the Cenozoic and repopulate the devastated Northern Hemisphere.

*Phalangiidae extend into the Southern Hemisphere in Africa, and Sclerosomatidae in South America, but in both cases it seems likely that these are more recent invasions from Northern Hemisphere ancestors.

The problem with a Gondwanan origin for the Phalangioidea, however, is that it implies a rather recent derivation for the Northern Hemisphere clade, within the last hundred million years or so, which seems a little out of kilter with the sedate rate of harvestman evolution suggested by the fossil record (most Eocene amber fossils [including Phalangioidea], for instance, can be assigned not only to modern families but even to modern genera). On the other hand, if sclerosomatids were present in the Middle Jurassic of China as suggested by Mesobunus, then that indicates that the modern phalangioid families had diverged before Gondwana had even properly divided from the rest of Pangaea, and some other explanation is required for modern phalangioid distribution.

REFERENCES

Dunlop, J. A. 2007. Paleontology. In Harvestmen: The Biology of Opiliones (R. Pinto-da-Rocha, G. Machado & G. Giribet, eds) pp. 247-265. Harvard University Press: Cambridge (Massachusetts).

Huang, D., P. A. Selden & J. A. Dunlop (in press, 2009). Harvestmen (Arachnida: Opiliones) from the Middle Jurassic of China. Naturwissenschaften.

Taylor, C. K., & G. S. Hunt. 2009. New genus of Megalopsalidinae (Arachnida: Opiliones: Monoscutidae) from north-eastern Australia. Zootaxa 2130: 41-59.

Of Taxonomy and Rabbis

noreply@blogger.com (Christopher Taylor) — Tue, 09 Jun 2009 01:31:00 +0000

A couple of weeks ago, Mike Keesey brought up a point where, it seems, the ICZN doesn't actually say what everyone has always thought it says. The tone of the ensuing discussion reminds me of a story that a Jewish friend of mine once told me. It concerns a disagreement that the famous rabbi Akiba ben Joseph* once had with a group of other rabbis on a point of law (hush up if you've heard this one before).

*Well, to be honest, I'm not sure if it was actually Akiba that was the subject of the story. It might have been some other influential figure. For the sake of maintaining a narrative, let's just say it was Akiba.

Anywho, the argument had apparently been raging for some time - Akiba holding out for one interpretation, all the other rabbis in the room holding to the other - and had evidently reached something of an impasse. Eventually, frustrated at his failure to get his point across successfully, Akiba exclaimed that if he was in the right, then the tree standing at the door of the synagogue should uproot itself and walk away. Amazingly, this is exactly what happened at that very moment. But the other rabbis were unimpressed by this miracle - after all, they demanded to know, what would a mere tree know of the Holy Law? Akiba then made another oath, that his correctness should be demonstrated by the river running outside the synagogue turning back on itself, and flowing uphill. Again, the river did this very thing (and according to the story, it still does today). But once more the other rabbis only scoffed - what does a river know of the Holy Law?

His frustration at a peak, Akiba appealed to the highest authority he knew of, exclaiming that if he was in the right, G-D himself would speak in his favour. And at the point, the clouds opened, a light shone down from the sky, and a great voice could be heard - "Rabbi Akiba is right!" Hearing this voice, the other rabbis turned to face the heavens, and spoke as one:

"And as for you - stay out of this!"

Saintly Harvestmen (Taxon of the Week: Equitius)

noreply@blogger.com (Christopher Taylor) — Mon, 08 Jun 2009 03:57:00 +0000

Features of Equitius formidabilis. Basically, a lot of spikes. From Hunt (1985).

The Australian harvestman genus Equitius was first named by the French arachnologist Eugene Simon in 1880. Now there was nothing particularly odd about that - for many years in the late 1800s, Simon was not so much an arachnologist as the arachnologist, achieving a reputation none of his contemporaries could match, and possibly none of his successors either (apparently, the Muséum National d'Histoire Naturelle still has his chair and desk on display). Simon used classical names for many of his genera, and Equitius was such a genus - there are numerous personages in Roman history by the name of Equitius, including an early Catholic saint. In this case, unfortunately, Simon seems to have dropped the ball somewhat in terms of getting the word out, because in 1903, the British researcher Pocock described a very similar species as belonging to a new genus, Monoxyomma. Then the baton was taken up by arachnology's favourite bête noire, Roewer, who in 1915 and 1931 added further genera, distinguished (as usual for Roewer) by the most superficial of features*, to the list. It wasn't until 1985 that the Australian Glenn Hunt combined all these genera into a single one, Equitius, found in southern Queensland and New South Wales.

*Hunt (1985) was later to refer to specimens for which the Roewerian system would have identified oneside as Equitius, and the other as Monoxyomma.

Equitius is a member of the Triaenonychidae, a family of Laniatores or short-legged harvestmen. Laniatores generally tend to be rather spiky, heavily-armoured creatures, but some triaenonychids have a tendency to be particularly baroque, with high spines ornamenting the eyemound and abdomen, and large spiny pedipalps in the males. The greatest diversity of triaenonychids has been described from Australasia (though southern Africa is fast catching up), and in my experience triaenonychids are the easiest harvestmen to find in New Zealand. That is, assuming that you can see them - they can readily be found by lifting logs and stones in moist areas, but the usual triaenonychid response when disturbed is to ball up their legs and freeze, at which point they become very difficult to spot against the background. Even if you do spot them, they still have the defense of the distinctive harvestman odour, which has on at least one occasion nearly (I stress nearly) fooled me into thinking that an individual I'd found was both dead and in a reasonably advanced state of decay.

An individual of a North American triaenonychid species, Fumontana deprehendor. Fumontana is something of a biogeographic enigma - despite its Appalachian distribution, it appears to be more closely related to Southern Hemisphere triaenonychids than to other North American species (which are quite possibly not correctly assigned to Triaenonychidae). Photo from the Marshal Hedin Lab.

One intriguing feature of a number of triaenonychid genera is the occurrence of male dimorphism, with one male form failing to develop the enlarged pedipalps and other secondary sexual characteristics of the other male form. In many similar cases in other animals, such male dimorphism is related to trade-offs between attractiveness to females and overall vitality, but it has not been demonstrated if that is the case with triaenonychids. Glenn Hunt studied the development of effeminate males in Equitius doriae for his PhD thesis, but unfortunately only the abstract was ever published (Hunt, 1981). Hunt found that effeminate males became dormant over winter an instar earlier than normal males, suggesting that dimorphism in this genus may be as much a matter of environmental factors as anything else.

REFERENCES

Hunt, G. S. 1981. Male dimorphism and geographic variation in the genus Equitius Simon (Arachnida, Opiliones). Dissertation Abstracts International B 41: 4375.

Hunt, G. S. 1985. Taxonomy and distribution of Equitius in eastern Australia (Opiliones: Laniatores: Triaenonychidae). Records of the Australian Museum 36: 107-125.

More on Drosophila and Sophophora

noreply@blogger.com (Christopher Taylor) — Fri, 05 Jun 2009 03:53:00 +0000

Before I start this post, a public service announcement. This month, a group of bloggers have joined together to present an initiative called Silence is the Enemy. The aim of this initiative is to raise awareness about the epidemic of sexual assualt faced by women in war-torn parts of Africa, and also to raise awareness about the issues of sexual assault in general. As part of this campaign, all those websites connected to it will be donating their proceeds from the month of June to Médecins Sans Frontières, which is working as we speak to bring aid and comfort to women affected by sexual assault (as well as bringing aid in countless other ways to people around the world who would otherwise be unable to obtain proper medical treatment). Contributing sites include The Intersection, On Becoming a Domestic and Laboratory Goddess, Bioephemera, Adventures in Ethics and Science, Aetiology, Neurotopia, The Questionable Authority and Drugmonkey. Every time you visit one of those sites in the coming month, you help to raise revenue for an extremely important cause. So visit early, visit often.

Now, on to today's post:

Some of you may remember this post from over a year ago, when the proposal was put before the ICZN to make Drosophila melanogaster the type species of the genus Drosophila. For this post, I'm going to take that other post as read. At the present point in time, the ICZN has not yet voted on that application. But this does not mean that things have been sitting unremarked - quite to the contrary.

As well as publishing applications to the ICZN and their results, the Bulletin of Zoological Nomenclature also publishes comments from the general taxonomic public on cases being considered, allowing other workers to put forward their arguments for whether the commission should accept or deny an application. To be quite honest, this is usually the dullest part of the Bulletin. The majority of applications are fairly straightforward, and it is fairly uncommon for comments to say anything much more extensive than either "sounds good to me!" or "No sir, I don't like it"*. The Drosophila case, however, has inspired a barrage of commentary in the pages of the Bulletin to a level that has probably never been seen there before. The June 2008 issue of the Bulletin included nearly fourteen pages of commentary on the application. Some of these "comments" bordered on being full articles - Prigent (in the June 2008 issue), for instance, filled up three full pages ("no sir, I don't like it"), while McEvey et al. (also June) put their names on two and a half pages ("no sir, I don't like it, but it should probably happen anyway"). [Disclaimer: I haven't yet seen the March 2009 issue of the Bulletin, but apparently it's got even more comments to read.] So what have been the main points raised for and against the proposal?

*This is not to say that the comments are completely pointless - for a start, they're probably the primary means for the commissioners to gauge the popularity or otherwise of an application. Still, the vast majority of them are not particularly likely to become citation classics.

A common complaint has been that supporting the decision would be to support a particular classification or method of classification (or, to put it another way, "Oh noes! They be taking my paraphylum!") As stated by Thompson et al. (June 2008):

The proposal declares that the current concept of Drosophila is 'paraphyletic' and thus 'violates modern systematic practice'. That practice is cladistics or Hennigian systematics. For followers of 'evolutionary' systematics or phenetics, paraphyletic taxa are acceptable. Then there are the issues of the utility of large and small taxa (i.e. lumping vs splitting). We feel strongly that the Commission should not be endorsing one classification paradigm over another.

Some of you may have been struck by the gratuitous conflations of phylogenetic and taxonomic methodologies in the second and third sentences there*, but let's ignore those for now and move on, shall we? It would indeed be a strong violation of the ICZN's principles to judge between paradigms (though I've previously questioned the possibility of a truly paradigm-free nomenclatorial system). In this case, however, the Commission is being asked to do no such thing. Those authors who wished to retain Drosophila melanogaster and D. funebris (the current type species) within a single genus, whether paraphyletic or not, would still be perfectly free to do so - from their perspective, the case is largely irrelevant. Even if an author wised to divide up Drosophila by non-cladistic means, then odds are that they would still end up wanting to place D. melanogaster and D. funebris, because the two species are about as different from each other as any taxa within Drosophila could be - that's why they've been placed in separate subgenera in the first place - and then we'd be facing the exact same question. Indeed, it could be argued (whether validly or not) that the current situation is the one impeding taxonomic freedom, because no-one has been willing to take the step of removing D. melanogaster from Drosophila. So overall, the "no paradigm endorsement" argument is dead in the water from the outset.

*I'm not sure that a phenetically-derived classification really can be said to "permit" paraphyly - it's more that for phenetics, questions of monophyly vs. paraphyly vs. polyphyly become irrelevant.

The second major argument is that changing the type species increases the amount of taxonomic instability rather than decreasing it. Unlike the first argument, this one actually has some legs. As I mentioned in the earlier post, the current subgenus Drosophila is considerably larger than the subgenus Sophophora to which D. melanogaster belongs. Therefore, making D. melanogaster the type species of Drosophila potentially means that more individual species will end up undergoing name changes than if the type species remained D. funebris. Also, while D. melanogaster is the most commonly used Drosophila species in research, it is not the only species used in research. A significant number of other species have also come under the microscope, and some of these other model species (such as D. virilis and D. mojavensis) belong to subgenus Drosophila rather than Sophophora. On the other hand, many more model species (such as D. simulans and D. yakuba) are also members of Sophophora, so changing the type species preserves their names in their current combinations as well.

From a purely taxonomic viewpoint (as many commenters have stated), the answer is a simple one - the current situation is clearly valid under the rules, nomenclatural changes are a perfectly valid part of an developing taxonomic system, there ain't nothing wrong with Sophophora melanogaster, whaddya complaining about? Unfortunately, the reason why this case was proposed in the first place was that such a change does not only affect taxonomists. The case is most elegantly summarised, I think, by McEvey et al.:

The binomen Sophophora melanogaster would continue to convey a precise meaning, and in this sense there would be no confusion. [However] With respect to nomenclatural instability, there may be considerable reluctance to adopt the unfamiliar binomen Sophophora melanogaster and many would, no doubt, continue using Drosophila melanogaster, Drosophila or just melanogaster. And this would be confusing. Information retrieval would be hampered.

Thompson et al. claim that such fears of confusion are overblown, and specifically cite the case of the mosquito Aedes aegypti, widely studied as a major disease vector, which has been renamed and almost universally accepted as Stegomyia aegypti in recent taxonomic revisions. This was perhaps the most comic moment in the affair to date, because as pointed out by van der Linde et al. in the December 2008 Bulletin, Aedes-errr-Stegomyia aegypti provides a very strong argument in favour of the application. Taxonomists have mostly accepted the name Stegomyia aegypti, but almost everyone else working on the beast - ecologists, parasitologists, epidemiologists - has rejected it, and continues to use the name Aedes aegypti. A wide rift has developed between the two sides, making communication between disciplines increasingly difficult. One should never underestimate the holding power a name can have if it somehow catches the public's imagination. After all, we still witness the occasional trotting out of Brontosaurus, a name that was in proper use for less than twenty-five years and was sunk into synonymy more than a hundred years ago.

So ultimately the question is whether preserving the names of a smaller number of economically significant taxa is more important than preserving those of a much larger number of taxa of less direct significance to humans. And I have to admit, I'm glad I'm not one of the people having to make an actual decision on this one.

REFERENCES

Linde, K. van der, G. Bächli, M. J. Toda, W.-X. Zhang, T. Katoh, Y.-G. Hu & G. S. Spicer. 2008. Comment on the proposed conservation of usage of Drosophila Fallén, 1823 (Insecta, Diptera). Bulletin of Zoological Nomenclature 65 (4): 304-307.

McEvey, S. F., M. Schiffer, J.-L. Da Lage, J. R. David, F. Lemeunier, D. Joly, P. Capy & M.-L. Cariou. 2008. Comment on the proposed conservation of usage of Drosophila Fallén, 1823 (Insecta, Diptera). Bulletin of Zoological Nomenclature 65 (2): 147-150.

Prigent, S. R. 2008. Comment on the proposed conservation of usage of Drosophila Fallén, 1823 (Insecta, Diptera). Bulletin of Zoological Nomenclature 65 (2): 137-140.

Thompson, F. C., N. L. Evenhuis, T. Pape & A. C. Pont. 2008. Comment on the proposed conservation of usage of Drosophila Fallén, 1823 (Insecta, Diptera). Bulletin of Zoological Nomenclature 65 (2): 140-141.

Focus on a Fern (Taxon of the Week: Polystichum vestitum)

noreply@blogger.com (Christopher Taylor) — Mon, 01 Jun 2009 02:12:00 +0000

The New Zealand fern Polystichum vestitum. Photograph by Alan Liefting.

For only the second time, the Taxon of the Week is going to be a single species. But while my earlier attempt at writing a Taxon of the Week post was hampered somewhat by a shortage of information about the species concerned, I'm happy to say that's not so much of a problem this time. And I'm also happy to say that for this post, I'm going home.

Polystichum vestitum (Forst.) Presl 1836, the prickly shield fern, is one of New Zealand's most abundant fern species. It's found in almost every corner of the country, including the Chatham and subantarctic islands, and even reaches as far south as Macquarie Island*. It is, however, restricted to the New Zealand biogeographic region - references in early sources to its presence in South America seem to represent confusion with Polystichum chilense (Looser, 1948). Polystichum vestitum is able to handle a greater deal of direct sun than other forest ferns, and is able to persist in cleared areas (Olsen, 2007). Mature specimens are about a metre in height and have a semi-tree fern growth habit, with a short trunk formed by the upright rhizome. Polystichum species are known as "shield ferns" because the stipes of the leaves are covered with glossy scales.

*Macquarie Island represents a obscure but interesting piece of the Great Trans-Tasman Rivalry. A small, windswept island halfway to Antarctica, almost untroubled by humans since the declines of sealing and whaling removed pretty much every reason why anyone would ever want to go there, Macquarie is biogeographically related to other subantarctic islands belonging to New Zealand, but is itself owned by Australia (in fact, it's technically part of the state of Tasmania, making Tasmania the third-longest Australian state north to south after Western Australian and Queensland). As a result, it's often covered in natural history works (such as bird field guides) for both countries. Despite having no trees, Macquarie Island is also notable for having been home to the world's southern-most parrot species, the parakeet Cyanoramphus erythrotis, until the effects of introduced animals caused their sudden decline and extinction in the late 1800s (according to Taylor, 1979, they survived dogs, they survived cats, but they were eventually undone by the rabbits**).

**The arrival of rabbits meant that the island was able to support higher populations of cats and also-introduced weka than it had previously, increasing the amount of predation by those species on parakeets beyond what the parakeet population could handle.

Another shot of Polystichum vestitum from NZ Plant Pics.

The scales of Polystichum vestitum are quite variable, and some authors have suggested that more than one species might be concealed under this name. Specimens found on the main islands of New Zealand have teardrop-shaped scales with broad bases and smooth edges, and with a glossy dark brown central region surrounded by a light brown margin. In many specimens from the Chatham and subantarctic islands, the scales become much longer, with a long trailing tip to the teardrop, and the dark brown centre disappears to leave an entirely light brown scale. In many Chatham Island specimens, the scales also develop notable marginal projections. However, these divergent morphologies are not universal in the outlying populations - instead, the populations vary from specimens with fully divergent morphologies to ones almost indistinguishable from mainland individuals. Analysis of the variation within Polystichum vestitum by Perrie et al. (2003b) failed to find clear divisions between the variants. When the variants were analysed using AFLP*** data, the fully divergent specimens from the Chatham Islands did cluster together, but with only low support, while the remaining specimens (including less divergent Chatham Island specimens) did not. Perrie et al. therefore recommended against recognising the divergent specimens as a distinct species or variety. However, it is remarkable that the level of variation in the small area of the Chatham Islands should be greater than that seen through mainland New Zealand. Perhaps an early population of P. vestitum became established on the Chathams and was partway into evolving into a new species but a second wave of colonisation from the mainland slowed things down? Multiple colonisations of the Chathams from the mainland have been demonstrated for another fern species, Asplenium hookerianum (Shepherd et al., 2009).

***Amplified Fragment Length Polymorphism - a method of observing variation in the sizes of the fragments that extracted DNA is chopped into by restriction enzymes. AFLP data is arguably a much rougher means of molecular analysis than full sequence comparison, but it has the distinct advantages of being much quicker and having a fraction of the cost, and hence also allowing comparison of a greater number of genes/alleles and individuals than would often be feasible with full sequencing.

The underside of a Polystichum vestitum leaf, showing the bicoloured scales. Photo by Larry Jensen.

In fact, the whole question of fern dispersal is an interesting one - as in, how much of it goes on? Ferns, of course, reproduce by means of spores which, being very small and light, could easily be carried long distances - perhaps even across oceans. It has therefore been suggested that distance has not been a major barrier in fern evolution. Brownsey (2001) suggested that most New Zealand ferns were derived from recent and common dispersals between Australia and New Zealand. In contrast, an AFLP analysis of Polystichum by Perrie et al. (2003a) found that the New Zealand species clustered in a clade, suggesting that they could possibly be derived from a single dispersal event. Interestingly, the closest relatives of the New Zealand clade were species from Lord Howe Island, which is positioned between Australia and New Zealand. Perrie et al. (2003a) also found specimens of another New Zealand species, Polystichum silvaticum, clustered together but were nested within specimens of Polystichum vestitum. This is in contrast to the results of Perrie et al. (2003b), which found a large distance between data from P. vestitum and P. silvaticum (but without data from other Polystichum species to provide a root). P. silvaticum shares the character of bicoloured scales with P. vestitum, but differs from it (and other Polystichum species) in lacking an indusium, a membrane that covers and protects young developing spores. Is it possible that P. silvaticum represents a derivative of P. vestitum?

And as a final aside, let me return to those subantarctic populations of Polystichum vestitum. On the Snares Islands, clumps of P. vestitum are apparently the preferred cover for nests of the Snares Island snipe, Coenocorypha huegeli (Miskelly, 1999). Why, you may ask, do snipes prefer to nest under ferns? As it turns out, birds on the Snares that nest higher up apparently lose a lot of eggs or chicks to petrels. Petrels don't eat the other birds, but they also nest under cover in the area - and petrels are notoriously bad at making landings. Touchdown for a petrel seems to basically involve throwing itself at the ground and hoping that there is enough vegetation to cushion its descent. Any nest in the way of a plummeting petrel is turned into kindling. In this situation, a nice sturdy fern is a ground-nesting birds friend, catching the petrels before they scramble your eggs.

REFERENCES

Brownsey, P. J. 2001. New Zealand's pteridophyte flora — plants of ancient lineage but recent arrival? Brittonia 53 (2): 284-303.

Looser, G. 1948. The ferns of southern Chile (conclusion). American Fern Journal 38 (3): 71-87.

Miskelly, C. M. 1999. Breeding ecology of Snares Island Snipe (Coenocorypha aucklandica huegeli) and Chatham Island Snipe (C. pusilla). Notornis 46: 207-221.

Olsen, S. 2007. Encyclopedia of Garden Ferns. Timber Press.

Perrie, L. R., P. J. Brownsey, P. J. Lockhart, E. A. Brown & M. F. Large. 2003a. Biogeography of temperate Australasian Polystichum ferns as inferred from chloroplast sequence and AFLP. Journal of Biogeography 30 (11): 1729-1736.

Perrie, L. R., P. J. Brownsey, P. J. Lockhart & M. F. Large. 2003b. Morphological and genetic diversity in the New Zealand fern Polystichum vestitum (Dryopteridaceae), with special reference to the Chatham Islands. New Zealand Journal of Botany 41: 581-602.

Shepherd, L. D., P. J. de Lange & L. R. Perrie (in press, 2009). Multiple colonizations of a remote oceanic archipelago by one species: how common is long-distance dispersal? Journal of Biogeography.

Taylor, R. H. 1979. How the Macquarie Island parakeet became extinct. New Zealand Journal of Ecology 2: 42-45.

Happy Birthday to Me (with Random Videos)

noreply@blogger.com (Christopher Taylor) — Wed, 27 May 2009 01:36:00 +0000

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)

noreply@blogger.com (Christopher Taylor) — Mon, 25 May 2009 06:14:00 +0000

The white-breasted waterhen, Amaurornis phoenicurus, one of the more widespread and distinctive Amaurornis species. Phot from here.

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 plain bush-hen of the Philippines, Amaurornis olivacea, type species and fairly typical of the brown species of the genus. Photo taken from here - and while you're at it, click through and take a look at the photo of the peacock-pheasant. Seriously, some birds are so incredible they just beggar belief.

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 brown crake, Limnocorax akool - long included in Amaurornis, but, it seems, not belonging there after all. Photo by Nikhil Devasar.

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.

John Gould's painting of Megacrex inepta - this flightless New Guinea bird may be an Amaurornis, or it may be something else entirely. Image from here - I don't normally link to sites selling stuff, but I suspect this one doesn't count as I doubt many of my readers have a spare $875 lying around to spend on a picture of a bird anyway.

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

noreply@blogger.com (Christopher Taylor) — Wed, 20 May 2009 03:55:00 +0000

The syllid worm Myrianida pachycera with a chain of developing epitokes. Photo by Leslie Harris.

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.

Some epigamous syllids brood their eggs after fertilisation, and may even retain the offspring after hatching. This is an illustration of one such syllid, Exogone rubescens, from here.

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)

noreply@blogger.com (Christopher Taylor) — Tue, 19 May 2009 01:31:00 +0000

Two species of the swordfish-like Cretaceous pachycormid Protosphyraena. This genus was not even closely related to the modern swordfish (contra Wikipedia), and represents a case of convergence. Reconstruction by Dmitry Bogdanov.

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.

Longnose gar, Lepisosteus osseus, one of the few living non-teleost neopterygians. Photo from here.

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.

Bowfin, Amia calva, the other survivor. Photo from here.

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.

The pycnodontiform Coelodus costai. Photo by Giovanni Dall'Orto.

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.

Figure from McCune (2004), showing a reconstruction of Semionotus, and variation in dorsal spine row morphology and overall body shape in Newark Semionotus.

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

noreply@blogger.com (Christopher Taylor) — Wed, 13 May 2009 04:15:00 +0000

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.

In Which I Blather On Elsewhere

noreply@blogger.com (Christopher Taylor) — Wed, 13 May 2009 03:27:00 +0000

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)

noreply@blogger.com (Christopher Taylor) — Mon, 11 May 2009 04:53:00 +0000

The minute marine gastropod Caecum (Fartulum) occidentale, all of 2.5 millimetres long. Photo by Maurio Pizzini.

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.

Caecum (Fartulum) magatama, even smaller at 1.8 millimetres. Photo from here.

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

noreply@blogger.com (Christopher Taylor) — Fri, 08 May 2009 13:25:00 +0000

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:

Crossing the Algal Divide

noreply@blogger.com (Christopher Taylor) — Wed, 06 May 2009 04:03:00 +0000

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.

Everything You Knew About Mayflies is Wrong (Taxon of the Week: Pisciforma)

noreply@blogger.com (Christopher Taylor) — Mon, 04 May 2009 03:18:00 +0000

Mayfly nymph of the pisciform genus Baetis (Baetidae). Photo by Jan Benda.

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).

Siphlonurus quebecensis (Siphlonuridae), another pisciform nymph. Photo from Troutnut.com.

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.

More Baetis nymphs. Photo by Surly Ghillie.

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.

A male baetid moulting into an imago. One of the easiest differences to spot between the submature subimagoes and the fully mature imagoes is that in the subimagoes the wings are generally opaque, while the imagoes have transparent wings. Photo stolen from Mick Hall.

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

noreply@blogger.com (Christopher Taylor) — Sat, 02 May 2009 12:13:00 +0000

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.

Ending Life in a Puddle of Ichor (Taxon of the Week: Coprinopsis herbivora)

noreply@blogger.com (Christopher Taylor) — Tue, 28 Apr 2009 04:57:00 +0000

This is an auspicious moment in the history of the Taxon of the Week series, because for the first time in nearly two years, the chosen taxon is an individual species rather than some more supraspecific. So you'd think I'd open the post with a nice big picture of the species in question, wouldn't you? Sorry, you'd be wrong, because I haven't been able to find a picture of Coprinopsis herbivora. In fact, I've been able to find next to diddly on Coprinopsis herbivora. All I've been able to establish is that it was described by Rolf Singer in 1973 from Argentina as Coprinus herbivorus (and I don't have access to the original publication), and it looks like it might be found worldwide: I've found references to what look like records from Australia and Finland. And as far as C. herbivora specifically goes, that is it.

Coprinopsis picacea. Like C. herbivora, C. picacea has been included in Coprinus subsection Alachuani (morphologically defined by the cellular structure of the cap), so the two species are likely to be closely related (NB. Because of the obscenely complicated way in which botanical subgeneric nomenclature works, I can't just say "Coprinopsis subsection Alachuani", because that name probably doesn't exist). Photo by Pau Cabot.

So let's widen the field of view a little. Those of you who didn't immediately recognise the names "Coprinopsis" and/or "Coprinus" were doubtless getting decidedly frustrated by the last paragraph, seeing as I had declined to mention just what, exactly, I was talking about. To explain, Coprinopsis and Coprinus are genera of mushrooms. Until recently, Coprinus included the mushrooms known as ink-caps. When an ink-cap first pops out from the ground, it looks like a fairly undistinguished mushroom. However, as the mushroom matures, the spore-bearing gills begin to liquefy. The mushroom's cap progressively dissolves into a puddle of vile black goo, like some sort of Z-grade horror effect. As the cap dissolves from the outside in, the spores mature in the same direction, so the progressive dissolution means that mature spores are always on the edge of the cap, well exposed to be caught and carried off by the wind. At least some species of ink-cap are edible (that is, if picked before they turn into sludge) but reports differ - many species contain a compound called coprine that can react violently with alcohol. To quote Edible Wild Mushrooms of North America: "It is important to note that coprine leaves the body primed for poisoning for several days (even a week by some reports) after eating the mushroom. Therefore, it is not only the consumption of a coprine-containing mushroom and an alcoholic drink at the same time that can cause coprine poisoning. Symptoms can also occur if someone drinks wine, for instance, two or more days after the meal or eats a coprine-containing mushroom after consuming alcohol" (emphasis in the original).

Another shot of Coprinopsis picacea specimens, showing various degrees of dissolution. Photo by Marino Zugna.

Well over a hundred species of Coprinus had been identified and described from around the world, but all that began to change in the late 1990s, with the advent of molecular phylogeny. A number of studies (most notably Hopple & Vilgalys, 1999) found that the genus Coprinus was polyphyletic, with at least two widely separated clades. The deliquescent cap, it turns out, had evolved on more than occasion. The great majority of species of Coprinus belonged to a clade containing other genera that had been assigned to the family Coprinaceae, though the Coprinus species were not monophyletic within this clade - the positions of species assigned to the genus Psathyrella divided them up into three smaller clades. A very small number of Coprinus species, however, fell within the family Agaricaceae, so more closely related to the common field mushroom Agaricus bisporus (i.e. the only mushroom that many British people and their equally mycophobic descendants are willing to believe is edible) than to other "Coprinaceae" species. This wouldn't have really been a problem, except that one of those agaricaceous defecters just happened to be the type species of Coprinus, C. comatus. This meant that the name "Coprinus" had to be associated with the small segregate, not with the clade containing the vast majority of species, and Coprinus went from including over a hundred species to including two or three. Similarly, the family containing that large clade could no longer be called Coprinaceae, because it no longer contained the genus Coprinus.

The taxonomic implications of all this were worked through by Redhead et al. (2001). They renamed the no-longer-Coprinaceae clade Psathyrellaceae, and divided the ex-Coprinus species into three genera corresponding to the three smaller clades found by Hopple & Vilgalys (1999). This was not an easy process, for a number of generic names had been synonymised with Coprinus over the years, and they all had to be checked to see if they applied to the "new" genera (the results are long and tortuous, and anyone reading Redhead et al., 2001, who does not have a particular enthusiasm for mycological taxonomy is likely to suffer severe cranial implosion). For two of the segregate genera, Coprinopsis and Coprinellus, Redhead et al. dredged up ancient and little-used generic names that had been used for species in each of these clades (and when I say ancient and little-used: Coprinopsis, for instance, had been named in 1881, its own author had abandoned it by 1889, and it had it never been used between then and 2001). The third clade had no suitable generic name, and so Redhead et al. proposed the new genus name Parasola. An older name, Pselliophora, did exist for the genus Redhead et al. dubbed Coprinopsis, but they recommended that that name be quashed - on the somewhat unsteady grounds that a change from "Coprinus" to "Coprinopsis" was easier to remember than one from "Coprinus" to "Pselliophora".

Coprinopsis xenobia, another member of 'Coprinus' subsection Alachuani. Photo by Hans Bender.

As can be imagined, the prospect of wholesale name changes for over a hundred species was not greeted with unalloyed enthusiasm from all quarters. While Redhead et al. put in their request for the conservation of Coprinopsis, Jørgensen et al. (2001) put in a counter-request to change the type species of Coprinus to a species in the largest of the segregate clades - Coprinopsis - so minimising the number of species needing name changes. The decisions on these proposals were published in 2005 (Gams, 2005), with what can only be described as a distinctly grumbling tone. The name Coprinopsis was conserved over Pselliophora - but it was made clear that this proposal would not have been supported if Redhead et al. (2001) had not gone ahead and published no less than 98 new combinations in Coprinopsis and so presented the Committee with something of a do-or-be-damned situation. The proposal to change the type species of Coprinus was turned down, on the grounds that, as well as being the type, Coprinus comatus is one of the better-known species in the old genus - and its vernacular name in French is "le coprin".

And can I note that this seems to be an extraordinary degree of kerfuffle over who gets to keep a name that, loosely translated into English, means "like a turd"?

REFERENCES

Gams, W. 2005. Report of the Committee for Fungi: 12. Taxon 54 (2): 520-522.

Hopple, J. S., Jr & R. Vilgalys. 1999. Phylogenetic relationships in the mushroom genus Coprinus and dark-spored allies based on sequence data from the nuclear gene coding for the large ribosomal subunit RNA: divergent domains, outgroups, and monophyly. Molecular Phylogenetics and Evolution 13 (1): 1-19.

Jørgensen, P. M., S. Ryman, W. Gams & J. A. Stalpers. 2001. (1486) Proposal to conserve the name Coprinus Pers. (Basidiomycota) with a conserved type. Taxon 50 (3): 909-910.

Redhead, S. A., R. Vilgalys, J.-M. Moncalvo, J. Johnson & J. S. Hopple Jr. 2001. Coprinus Pers. and the disposition of Coprinus species sensu lato. Taxon 50 (1): 203-241.

Singer, R. 1973. Diagnoses fungorum novorum Agaricalium. III. Beihefte zur Sydowia 7: 1-106.