By Christopher Taylor at 12/27/2007 12:23:00 pm
Hi peoples, it's Circus of the Spineless time again, making its first ever appearance here at Catalogue of Organisms! (The act is being headlined by a spectacular clearwing butterfly from Jennifer Forman Orth.) A reminder, too, that the next edition of Linnaeus' Legacy will be appearing in a week's time - get your submissions in to Greg Laden by the 5th of January!
And what would a circus be without some music? It suddenly occurs to me that I should have written the song earlier and gotten Kevin Zelnio to record a performance of it, but I didn't, and you're all just going to have to hum it to yourselves, to the tune of The Beatles' For the Benefit of Mr. Kite.
For the benefit of spineless beasts, tonight we have a major feast
With all the corals there could be, polyps waving in the sea,
Aren't they great?
Deep-Sea News and The Other 95% have decided that nothing says Christmas more than a squishy bag of jelly with tentacles - especially if they come in flourescent green and red colours!
Predators and prey compete, with fungal lassos formed from hyphal threads!
Leaving signs that this sort of thing has happened for years!
Not Exactly Rocket Science has two studies for us on past and present interactions between inverts and their enemies. In the first, water fleas and their parasitic bacteria that have lain dormant in mud for up to 39 years have been revived to test how interactions between the two have changed over time, the bacteria evolving increased ability to infect while the the water fleas increase their ability to resist infection.
In the second, fossil remains have been found in Cretaceous amber of fungal hyphae forming "lassos" to catch nematodes for nutrition. Most interestingly, the fungus in question seems to belong to a different line than the Orbiliaceae, the modern practitioners of the art!
Insects supply a drongo's feast, though the beetles are a sight to see,
the spiders too.
Follow the links for pretty pictures from Bird Ecology Study Group and Ben Cruachan.
The snails gayly fornicate, able to know their suited mate,
We've not a clue.
Pascal, the author of Research at a snail's pace reports that two of his snails have mated, leaving him hopeful for a litter of little snail-lets. One of the happy pair kicked it a few days after mating, which is something of a benefit to Pascal, because he wasn't able to properly ID them to species without cutting them open and looking inside.
Toronto has a warning out, there's beetles on the move that spread disease
And that is something we don't want at all!
The assassin bug will knock you down, displaying its amazing gown
Of ant remains.
Go to The Other 95% to learn how one species of assassin bugs coats itself in the drained husks of the ants it feeds on in order to elude its own predators!
And if you want a nudibranch, and have a fair bit in the bank,
then stake your claim!
Finally, Jim Lemire has been made a little unhappy by an institute reduced to auctioning off the naming rights to a pile of new species in order to pay the bills.
Farewell Circus of the Spineless, we hope that you enjoyed the fun this month!
Next round, see Andrea's Buzzing About!
Additional photo credits: Nematode trapped by a fungus from Neatorama. Snail porn from Wikipedia. Latest assasin bug fashions from Jackson & Pollard (2007).
Update: Two submissions from Susannah at Wanderin' Weeta failed to get through to me in time. If you go here and here, you can help her try to identify some mystery organisms.
By Christopher Taylor at 12/23/2007 07:30:00 pm
This week's highlight taxon is going to be a fairly cursory affair, for reasons that I think should be obvious. Indeed, for the same equally obvious reasons, posting is going to be fairly intermittent here over the next few weeks. There's Christmas coming, and then Jack and I are off to Adelaide for a couple of weeks (if anyone has recommendations for things to do in Adelaide, feel free to pass them on). Anywho...
Cotoneaster is a genus of shrubs (occassionally small trees) native to the Palaearctic, but also present in other temperate areas as represented by weed species. As shown pretty well in the photo of a Cotoneaster frigidus specimen above (from Wikipedia), Cotoneaster is part of the Rosaceae and closely related to such genera as Crataegus (hawthorns) and Pyracantha (firethorns). Depending on how you look at it, Cotoneaster is a smallish genus or a rather large genus. The problem is that a number of polyploid lines of Cotoneaster are avid indulgers in apomixis, the asexual production of seed (plant parthenogenesis). The resulting shortage of genetic recombination means that there is almost no theoretical limit to how minutely the 'species' can be divided, and a whole host of 'microspecies' of perhaps dubious practicality potentially can be (and often have been) identified. The situation is even further complicated in many plants such as Cotoneaster that are not obligate apomicts - Cotoneaster flowers remain attractive to wasps, and a very low level of sexual reproduction may still occur. Most authors, though, continue to define their Cotoneaster 'species' fairly broadly, in a victory for pragmatism over precision.
By Christopher Taylor at 12/22/2007 08:12:00 pm
I'll be hosting the next installment of Circus of the Spineless next week on the 27th. A number of submissions have already come in, but there's always room for more. So if you have put up anything related to the invertebrate majority, get them in to me by then!
By Christopher Taylor at 12/21/2007 10:29:00 am
Heenan, P. B. 1996. A taxonomic revision of Carmichaelia (Fabaceae - Galegeae) in New Zealand (part II). New Zealand Journal of Botany 34: 157-177.
I have a suspicion that New Zealand does not have one of the most diverse floras by world standards overall. However, one can't help noticing that within the New Zealand flora, certain genera seem to make up disproportionate numbers of species. Genera such as Hebe (ermmm... Veronica?) and Coprosma seem to have undergone speciation explosions and can be found almost anywhere you'd care to go. With a little over twenty species, the New Zealand brooms of the genus Carmichaelia (C. flagelliformis shown above, from Wikipedia) are not quite in Hebe league, but still represent a quite respectable little radiation. Except for a single species on Lord Howe Island between New Zealand and Australia, the Carmichaelia species are restricted to New Zealand. In the past a number of smaller genera of New Zealand brooms were recognised in addition to Carmichaelia, but phylogenetic analysis indicates that these groups are nested within Carmichaelia (Heenan, 1998), so they have no all been synonymised with the larger genus. Unfortunately, a significant number of Carmichaelia species are endangered or vulnerable, as they seem to favour habitats that are prone to human disturbance.
Prior to Heenan's work in the mid-1990s, Carmichaelia taxonomy was a bit of a mess. More than fifty species had been named at one time or another, mostly from individual collections. Heenan seems to have conducted something of a slash-and-burn, reducing the number of species from over fifty to seventeen (Heenan, 1995, 1996). When studied at more of a population level, some of the Carmichaelia species turned out to be decidedly variable - the extreme being Carmichaelia australis, which swallowed up some twenty-five synonyms, showing noticeable variation in seed and seed-pod size, shape, colour and growth habit. In the latter case, Heenan demonstrated that this represented true intra-specific variation rather than lumping of different species under one name by examining a single population in Canterbury along a transect of 150 metres, and showing that variation in seed-pod size and shape in the one population was as great as in the population as a whole. One population of C. australis had previously been described as a separate species due to its spreading growth habit, rather than erect as in other populations - however, when plants from this population were grown in cultivation they adopted the erect habit of other C. australis, indicating that the habit found in the wild was due to environment.
The biogeographical implications of Heenan's work are rather interesting. While C. australis, for instance, is found almost throughout New Zealand, other species have exceedingly restricted ranges. I've spoken before (see here and here) on the phenomenon of restricted soil types resulting in equally restricted plant species, and Carmichaelia provides more examples. The prostrate C. appressa, for instance, is restricted to sandy soils and dunes on the Kaitorete Spit in Canterbury. Heenan suggests that C. appressa may represent a segregate from C. australis (from which it differs only in growth habit and the colour of its cladodes [photosynthetic stems]) that has adapted to the different soil, and phylogenetic analysis (Heenan, 1998) does place C. appressa as the sister to C. australis. Heenan also records two other populations from different localities in Canterbury that are very similar to C. appressa, but refrains from actually assigning them to that species, alluding to the possibility that these may prove to be independent segregates from C. australis that have convergently developed the characters of C. appressa in adapting to similar habitat.
Carmichaelia hollowayi (shown at left in a photo by John Barkla from New Zealand Plant Conservation Network), in contrast, is restricted to limestone soils, and is known from only three outcrops of the Otekaike limestone in northern Otago, with very low numbers at each site. Heenan (1996) recorded that the largest of the three populations numbered about 45 individuals, while the smallest contained only three. Seedlings or young plants were not found at any site, and appeared to be excluded by introduced pasture grasses and weeds.
Still, some aspects of Heenan (1996) just scream out for further research. I've already mentioned the C. appressa conundrum. Another species, C. odorata, exhibits what Heenan interprets as a clinal variation across its distribution from north to south, but an uninhabited band through central Nelson divides its distribution in half. Are the northern and southern populations taxonomically distinct? Heenan points out that while the range of variation in each population is distinct, some overlap occurs.
I've also already referred to changes in growth habit due to environment in C. australis. Carmichaelia petriei also shows variation in growth habit, with both erect and prostrate forms in the wild. Cuttings of the prostrate form taken into cultivation develop the erect habit, arguing against taxonomic distinction and suggesting the prostrate habit is environmentally induced. However, the same area in the wild may contain both prostrate and erect individuals, so what is going on? Has the prostrate form only evolved recently, and potentially-prostrate individuals have not yet displaced obligately-erect individuals from prostrate-favouring habitat?
Finally, I can't help feeling that a re-division may still occur of C. australis. While some features such as pod size and shape have been shown to vary within individual populations, others such as cladode form do still vary geographically. Heenan refers to research by Purdie (1984) that identified geographical variation in flavonoid chemistry in what would become C. australis (but then represented multiple species). This is interesting, as flavonoid chemistry has some taxonomic significance in other plants (e. g. Bayly, 2001). However, Purdie did not provide voucher specimens of the species he used, reducing the taxonomic usefulness of his results (the variation did not fully match up with species boundaries as recognised at the time). One more example of the extreme importance of providing voucher specimens in any ecological study!
Bayly, M. J., P. J. Garnock-Jones, K. A. Mitchell, K. R. Markham & P. J. Brownsey. 2001. Description and flavonoid chemistry of Hebe calcicola (Scrophulariaceae), a new species from north-west Nelson, New Zealand. New Zealand Journal of Botany 39: 55-67.
Heenan, P. B. 1995. A taxonomic revision of Carmichaelia (Fabaceae – Galegeae) in New Zealand (part I). New Zealand Journal of Botany 33: 455-475.
Heenan, P. B. 1998. Phylogenetic analysis of the Carmichaelia complex, Clianthus, and Swainsona (Fabaceae), from Australia and New Zealand. New Zealand Journal of Botany 36: 21-40.
Purdie, A. W. 1983. Some flavonoid components of Carmichaelia (Papilionaceae) — a chemotaxonomic survey. New Zealand Journal of Botany 22: 7-14.
By Christopher Taylor at 12/18/2007 01:10:00 pm
Valdecasas, A. G., D. Williams & Q. D. Wheeler. 2007. ‘Integrative taxonomy’ then and now: a response to Dayrat (2005). Biological Journal of the Linnean Society 93 (1): 211-216.
Before I start this, I feel I should perhaps slap a 'Parental Advisory' warning on it. The link to this article turned up in a Table of Contents e-mail alert a moment ago, and it's gotten me feeling a little steamed up. Not by what was said by Valdecasas et al. - I agree with almost everything they had to say - but with the article they were rebutting.
The question behind both articles, ultimately, is the current Taxonomy Crisis - essentially, the fact that there are just too many undescribed species and not enough work being done to identify them. I've written about it before (or just click on the "principles of biodiversity" label attached to this post), so I'll refrain from explaining in detail again. Dayrat (2005) argues that in order to escape this crisis, we need a significant rehaul in how we do taxonomy. However, as Valdecasas et al. (2007) point out, some of his suggested 'solutions' would probably end up doing more harm in the long run than good.
Dayrat's call for a more 'integrative taxonomy' translates into the call for taxonomists to work more closely with molecular ecologists and population biologists in establishing species boundaries. In this, he is presenting us with a bit of a truism. It is certainly true that new species should be established on the basis of as much data as possible, and I don't believe any working taxonomist would argue with this. However, this should be an enabling, not a limiting, factor. As much as we would all love to have all that wonderful data when conducting our species revisions, the simple fact is that sometimes (probably even more often than not) we can't count on it. In such cases, surely it is better to go ahead with what data you have available, rather than allow your work to languish indefinitely while you wait for extra data that may never show. Valdecasas et al. provide a quote from Bonde (1977) that rather summarises my feelings on the subject: "An important aspect of any species definition whether in neontology or palaeontology is that any statement that particular individuals (or fragmentary specimens) belong to a certain species is an hypothesis (not a fact)" (emphasis my own).
Dayrat complains that the 'over-abundance of redundant species names' (synonyms and nomina dubia) is a major impediment to taxonomy (a nomen dubium, for anyone not in the know, is a taxonomic name for which not enough data is available to firmly establish to what species, etc. it originally referred). His implication is that to much time is being wasted on sorting out these 'redundant names' that should be spent on describing new species. It is true that the ICZN currently does not officially allow for a potential nomen dubium to be set aside for a better characterised later name, but there is a very good reason for that - namely, that the recognition that a name is a nomen dubium is entirely dependent on context, and to a certain degree on author preference. There is no objective standard to what constitutes 'enough data'. What is sufficient in one case may not be in another. Besides, Dayrat is overlooking the historical context of many, if not most, nomina dubia. While they may not be regarded as identifiable now, at the time they were described many such taxa were different from all that had been known to that date, and the original authors can hardly be blamed for failing to predict that their 'unique' new specimen would turn out to be not so unique. I find it a little ironic that Dayrat complains of the "typological approach" of taxonomists, yet speaks favourably of DNA barcoding, a more typological method than almost anything commited by any morphologist (well, except Carl-Friedrich Roewer).
For instance, it is a general rule of thumb in vertebrate palaeontology that taxa based on reptile teeth are not diagnostic, because teeth do not vary enough between species of reptiles. Nevertheless, Troodon formosus (shown at top in a reconstruction from here) was originally based on a tooth, and yet it can be identified as a species with other specimens because there happens to be only one species known from the type locality with that kind of teeth. Of course, the possibility always exists that another species will turn up in the same locality with the same sort of teeth, in which case the identity of the original Troodon becomes uncertain. But I feel that there's little point in playing such 'what if' games - I refer the reader back to the Bonde quote above.
Let's move on to the details of Dayrat's recommendations:
"No new species names should be created in a given group unless a recent taxonomic revision has dealt with the totality of the names available for the group." Valdecasas et al.'s primary response to this is "define recent". Many groups have not been substantially revised for a great many years (for instance, the last complete review of many harvestman families was probably Roewer's Die Weberknechte der Erde in 1923). Still, many of these ancient revisions are still considered very reliable due to the thoroughness of the original author. Even when there isn't a good revision available, this may not be an impediment to taxonomic work. Revising an entire group is a major task, and making it the minimum expectation will simply cause researchers to shun poorly studied groups, leaving them to languish in their taxonomic pits. The taxonomic crisis would then worsen rather than improve.
As a point of contrast, I have commented before on the systematic quagmire of South American harvestmen. For a number of years now, a colony of South American arachnologists have slowly been chipping away at this heaping mess, sorting out issues where they could. As a result, parts of the picture are slowly coming into view, and there is hope for more unravelling to come (e.g. Kury, 2003). It is true that some findings have been published as separate papers that could have arguably been included in the same publication (an artefact, I believe, of an academic accreditation system that values total number of publications to the individual quality of said publications), but overall the value of their work is, I think, unarguable.
"No new species names should be created if the infra- and interspecific character variation has not been thoroughly addressed." This is directly connected to the following recommendation: "No new species names should be created based on fewer than a certain number of specimens (a number which specialists of each group could agree upon), and never with a single specimen." Again - how many is enough? Is a species based on a single, very distinctive specimen necessarily less reliable than one based on a number of specimens but very similar to another, already named specimen? Valdecasas et al. argue the cases of fossil or endangered species, where the researcher may not be able to count on obtaining further specimens. If you have a distinctive and probably new taxon, surely it is better to bring it to attention rather than, again, letting it languish? Which brings us to:
"A set of specimens differing in some regard from existing species can be described with the abbreviation 'sp.' (for 'species') and not with a real species name regulated by the codes of nomenclature." Technically true, but not so hot in practice. Dayrat is overlooking that 'sp.' is often used in species lists to indicate specimens that can be identified to a genus but not to one of the species within a genus - usually, with the implication that the specimens cannot be reliably identified. Also, Dayrat is overlooking the power that names have when catching people's memory. Things named 'sp.' slip into obscurity, while taxa with actual names hold their place. Witness how even when a taxon becomes widely known (say, as a conservation target) before it gets officially described, the need to label it with a tag is inescapable. The Mahoenui giant weta was appearing as 'Deinacrida sp. Mahoenui' long before Deinacrida mahoenui was officially published. And because there are no regulations governing the use of such informal tags, they cause more confusion if allowed to persist without a suitable official replacement than otherwise.
"Ideally, names should only be created for species that are supported by broad biological evidence (morphology, genealogical concordance, ecology, behaviour, etc.)." Again, this is true, but how broad? As Valdecasas et al. point out, there is no upper limit to how much data could potentially be collected. Again, surely it's better to highlight the fact that an interesting new taxon potentially exists than to allow it to remain hidden?
"No new species names should be created if type specimens deposited in a museum collection are preserved in a way that prevents any further molecular study." Also: "All neotypes designated from now on should be preserved in a way that allows DNA extractions and sequencing." Aaaaaaaaaaaargh! NO! Dayrat is overlooking that retaining specimens for molecular analysis often renders them unusable for other forms of analysis. If I was collecting arachnid specimens, I would have to decide on collection whether to put it into 70% alcohol or 100% alcohol for preservation. In 70% alcohol, the specimen's morphology remains preserved, but DNA degrades fairly rapidly because of the presence of water. However, if I was to put the specimen in 100% alcohol, the absence of water dessiccates all membranes, rendering the specimen brittle and immobile, unusable for morphological analysis. The problem is even worse for entirely soft-bodied animals, which may shrivel in 100% alcohol to unidentifiable lumps. In the case of arachnids, the researcher may get around the problem by preserving most of the specimen in 70% alcohol, but remove a couple of legs and put them in 100%. But what would s/he do if s/he was working on rotifers, or some other minute organism? The appropriate means of preservation should be dictated by the requirements for identifying the particular taxon, not by any theoretical standard.
Ultimately, the problem with Dayrat's suggestions is that he is confusing the position of the donkey and the dray. Ultimately, the recognition of a new species is a hypothesis based on a collection of data to be tested by further data, not a data point in itself. If a set of objective 'minimum requirements' is imposed, it will probably have the negative effect of discouraging research and publication, and the taxonomy crisis will worsen rather than improve. 'Minimum requirements' may sound good in theory, but practical considerations speak otherwise. As Valdecasas et al. note, "In any case, experience demonstrates that it is far more detrimental to be a ‘lumper’ than a ‘splitter’, in contrast to Dayrat's assertion. If variation previously assigned to two species turns out to be more economically assigned to one, synonymy of subsequently identified specimens will easily solve the problem. When the same name has been given to specimens that exhibit enough variation to include several species, it is considerably more difficult to recover in subsequent work which identifications correspond to which species unless there is a repository of all specimens; and that is not always the case, as it is very common in much ecological work to refrain from preserving the specimens upon which the identifications were based, leaving no option for further rigorous identification." The taxonomy crisis will not be resolved by imposing outside standards (which incompetent workers will ignore anyway), but by knuckling down and describing species.
Bonde N. 1977. Cladistic classification as applied to vertebrates. In Major Patterns in Vertebrate Evolution (M. K. Hecht, P. C. Goody, & B. M. Hecht, eds.) pp. 741-804. Plenum Press: New York.
Dayrat, B. 2005. Towards integrative taxonomy. Biological Journal of the Linnean Society 85 (3): 407-415.
Kury, A. B. 2003. Annotated catalogue of the Laniatores of the New World (Arachida, Opiliones). Revista Ibérica de Aracnología, special monographic volume 1: 1-337.
By Christopher Taylor at 12/18/2007 10:28:00 am
Of all the groups of unicellular or paucicellular (excuse the neologism) eukaryotes generally lumped under the heading of 'protozoa' or 'protists', ciliates are one of the most noteworthy. Together with sporozoans, they were one of the very few groups to be recognised as distinctive* before the microbial classificatory revolution that was permitted by the appearance of SEM and molecular phylogeny. Through the example of Paramecium, they are also one of the few protist groups whose existence is widely known by the general public. While other prostists such as many flagellate** groups tend to be morphologically fairly plain, ciliates attain a diversity of form and complexity that seems incredible for unicellular organisms.
*Except for an unfortunate tendency for the non-ciliate Stephanopogon to keep trying to mooch its way into the ciliate party. Researchers still have pretty much no idea what to do with Stephanopogon, but the ciliates are adamant that they want nothing to do with it.
**Pre-revolution classifications generally divided protozoans on the basis of locomotory structures between flagellates (with flagella), amoebae (pseudopods), ciliates (cilia) and sporozoans (parasitic taxa without locomotory structures). While it is well-recognised by now that these divisions are largely artificial*** (as is the term 'protozoa' itself), they retain a certain degree of utility as descriptive conveniences (as does 'protozoa'), though 'amoeba' should probably be passed over for 'amoeboid' so as not to cause confusion with the actual genus Amoeba. Also, while light microscopists distinguished flagella (relatively long and few) and cilia (relatively short and usually arranged in tracts), there is no real difference between the two. Some researchers would prefer to refer to all such structures in eukaryotes as 'cilia', reserving the term 'flagella' for bacterial locomotory structures, which are very different.
***Especially as many protists have both amoeboid and flagellate stages in their life cycles.
While the new technologies allowed ciliates as a whole to retain their integrity, they did incite a bit of reshuffling within the clade. Earlier classifications emphasised features of the oral apparatus, but from the 1980s the importance of ultrastructural characters such as arrangement of cilia was recognised (Lynn, 2003). With the addition of molecular data, the ciliates settled (a little uneasily) down into eleven or so classes, some of them well-supported by both molecular and morphological data, some by only one or the other. It is with one of these classes, the Spirotricha, that we concern ourselves today.
The Spirotricha are a diverse bunch, and support for them as a total group is, admittedly, fairly low (though support increases if the divergent Protocruzia is left out of the mix). The classic feature of the spirotrichs are the cirri - bunches of cilia fused into tendril-like structures, which can be seen fairly well in the photo at the top of the post of Euplotes (from A Micronaturalist's Notebook. Not all taxa united molecularly with spirotrichs possess cirri, but features of macronuclear* division also support the grouping.
*An individual ciliate possesses multiple nuclei - one small micronucleus and one or more larger macronuclei. The macronuclei are involved in the day-to-day production of enzymes and such, while the micronucleus is involved in reproduction. When conjugation (sexual reproduction) occurs, the macronuclei break down and only the micronucleus is propagated. The macronuclei are then regenerated from the daughter micronuclei (see here for a more detailed and accurate description - like many so-called 'simple' organisms, ciliates make up for simplicity of structure by indulging in obscenely complicated life cycles).
Euplotes is one of the best-known of the spirotrichs. The photo above well illustrates how Euplotes uses its cirri to walk along the substrate, though they can also be used for swimming. Euplotes is a predator of other ciliates, and as such has a rather large oral cavity. Its voracity in feeding can be remarkable - Kloetzel noted in 1974 that "In extreme cases (with small Tetrahymena, which are eaten much more rapidly than large ones) a Euplotes cell can ingest 17 Tetrahymena within 5 min, representing an area of food vacuole membrane approximately twice that of the entire Euplotes surface". Trust me, I'm fighting the urge to add exclamation marks after that one.
Spirotrichs also include the only ciliate group to have a significant fossil records, the tintinnids. Unlike other ciliates, tintinnids form a lorica (a vase-shaped shell) that may be preserved after the death of the organism (shown above in an SEM by Fiona Scott from Australian Antarctic Division). A detailed taxonomy exists of tintinnids based mainly on lorica structure and composition, and it has been suggested that tintinnids with agglutinated loricas are basal to those with hyaline loricas. However, studies based on living tintinnids show that different lorica types may be possessed by species with the same or similar ciliary arrangements, and there does not appear to be a close correlation between lorica structure and ultrastructure of the living organism (Agatha & Strüder-Kypke, 2007).
Agatha, S., & M. C. Strüder-Kypke. 2007. Phylogeny of the order Choreotrichida (Ciliophora, Spirotricha, Oligotrichea) as inferred from morphology, ultrastructure, ontogenesis, and SSrRNA gene sequences . European Journal of Protistology 43 (1): 37-63.
Kloetzel, J. A. 1974. Feeding in ciliated protozoa. I. Pharyngeal disks in Euplotes: a source of membrane for food vacuole formation? Journal of Cell Science 15: 379-401.
Lynn, D. H. 2003. Morphology or molecules: How do we identify the major lineages of ciliates (phylum Ciliophora)? European Journal of Protistology 39 (4): 356-364.
By Christopher Taylor at 12/13/2007 12:20:00 pm
Skovgaard, K., S. Rosendahl, K. O’Donnell & H. I. Nirenberg. 2003. Fusarium commune is a new species identified by morphological and molecular phylogenetic data. Mycologia 95(4): 630-636.
Fusarium is a genus of filamentous soil fungi (shown above in a diagram from here) that is best known as a cause of a selection of nasty diseases of crop plants. It is an anamorphic genus - that is, it includes taxa that reproduce asexually. Fungal taxonomy maintains a complicated system of classifying asexual anamorphs separately from sexual teleomorphs, at least at the generic level (for instance, Fusarium anamorphs are associated with various teleomorphs of the family Nectriaceae - Rossman et al., 1999). In the past, there were separate families and higher for anamorphic taxa, but these have largely been abandoned. This system remains in place despite the fact that some "individual" hyphal masses (inasmuch as one can recognise an individual in fungi) may reproduce both asexually and sexually. In a previous post, I commented that the double taxonomy system was due to a "combination of history, theory and a certain degree of pragmatism". Anamorphs are usually completely different in appearance to teleomorphs, and there is generally no way to tell easily whether a given teleomorph corresponds to a given anamorph (usually, the only way to make a connection is to luck out and find one of the double-dipping hyphae I refered to a moment ago). Even when a connection is made, there is not necessarily a one-to-one relationship between anamorph and teleomorph - one anamorph may correspond to more than one teleomorph. There are even cases known where an anamorphic taxon is found worldwide, but its apparent teleomorph is only known from a very restricted location. A theoretical component can be invoked, too - species concepts are supposed to reflect gene flow, and gene flow is generally not occurring between anamorphic and teleomorphic lines. There are issues with the double taxonomy system, of course - perhaps most significantly, anamorphic taxa seem to be something of the poor cousins of mycology. Despite their being far more abundant in the environment, anamorphs seem to receive only a fraction of the attention given to their more glamorous teleomorphic counterparts.
I think it's worth noting that almost all anamorphic taxa are treated as essentially artificial form-taxa. Thus, while Fusarium seem to all fall within the Nectriaceae, there is no assumed guarantee that taxa with a Fusarium anamorph necessarily form a monophyletic unit. One teleomorphic genus may include members with a number of different anamorphic forms, that each may be shared with members of other teleomorphic genera. Attempts to try to restrict anamorphic genera phylogenetically, such as Sampaio et al. (2003), are relatively few and far between.
With that background explanation dealt with, on to the description of Fusarium commune Skovgaard et al., 2003. One of the big problems with taxonomy of anamorphic is that, well, there's often not that much to work with. All the flashy characters, the colourful mushrooms, the pungent truffles, the wierd-shaped fruiting bodies, are sexually-reproducing structures of teleomorphs. When a fungus is not actively fruiting, one collection of hyphae looks much like another. And conidia, the structures that give off asexually-produced spores in anamorphs, are often not much more than budding extensions of hyphae. As a result, useful morphological characters of anamorphs are few and often somewhat vaguely distinguished.
It should therefore come as no surprise at all that when molecular data was applied to anamorphs, it seemed that the amount of diversity present had been significantly underestimated. Convergence in anamorphs is rampant, and two morphologically near-identical samples may easily turn out to be very distant phylogenetically. So when morphological taxonomy has proven insufficient, in steps the substitute of molecular taxonomy. And that, I'm afraid, is where my hackles start to raise themselves just a little.
The use of molecular data in taxonomy is a much-abused field. Generally speaking, molecular data cannot resolve species. Any analysis of molecular data results in a branching tree, but species identifications are supposed to be about identifying gene flow in networks. There is no magic figure for "x% genetic divergence = different species". A single species with a large, widespread population (say, a wide-ranging bird species) may feature a large amount of genetic divergence without barriers to gene flow. In contrast, a cluster of short-range endemic species (e.g. snails that don't move about much at all) may have very little genetic variation within or even between populations without gene flow occurring between them. So any use of molecular taxonomy should be approached with extreme caution.
I'm glad to say that Skovgaard et al. seem to get it mostly right as far as I can tell. They use 15 different isolates of the new molecular species - a very important step in fending off the spectre of sample contamination. And they also identify some morphological traits supporting the new species. Fusarium commune differs from the closely related F. oxysporum in producing polyphialides and long, slender monophialides when grown in the dark*, while F. oxysporum produces short monophialides only (phialides are the hyphal branches that produce conidia - if I interpret correctly, polyphialides produce spores in multiple axes, while monophialides only have one axis). I am a little mystified as to why there are no samples of F. blasticola, referred to in the article text as very similar to F. commune, included in the molecular analysis. However, Skovgaard et al. do demonstrate the distinction of F. commune from F. blasticola through a pathogenicity test. Fusarium blasticola is a pathogen of Picea (spruces) and Pinus (pines). Despite specimens of these two hosts being grown for five months in soil inoculated with cultures of F. commune, no sign of infection was noticed. Fusarium commune has since been shown to be able to cause infection in Pseudotsuga (the Douglas fir), another commercial conifer (Stewart et al., 2006).
Rossman, A. Y., G. J. Samuels, C. T. Rogerson & R. Lowen. 1999. Genera of Bionectriaceae, Hypocreaceae and Nectriaceae (Hypocreales, Ascomycetes). Studies in Mycology 42: 1-248.
Sampaio, J. P., M. Gadanho, R. Bauer & M. Weiss. 2003. Taxonomic studies in the Microbotryomycetidae: Leucosporidium golubevii sp. nov., Leucosporidiella gen. nov. and the new orders Leucosporidiales and Sporidiobolales. Mycological Progress 2(1): 53-68.
Stewart, J. E., M.-S. Kim, R. L. James, J. R. Kasten Dumroese & N. B. Klopfenstein. 2006. Molecular characterization of Fusarium oxysporum and Fusarium commune isolates from a conifer nursery. Phytopathology 96 (10): 1124-1133.
By Christopher Taylor at 12/12/2007 05:37:00 pm
This week's highlight taxon (sorry it's a little late, my partner's been sick) is the Rhynchonellata. Rhynchonellata are one of the major clades of the brachiopods, marine animals that look rather like bivalves (clams, mussels, etc.) on the outside, but completely different on the inside. Textbooks will usually tell you that brachiopods are commonly known as "lamp shells" (supposedly because the shell of some species bears a vague resemblance to an archaic lamp), but I can't say as I know if anyone actually uses that name. Rather, as with bryozoans supposedly being "moss animals", this seems to be a name promulgated in textbooks only. Anybody actually interested enough to discover the existence of brachiopods is usually interested enough to not be too scared by technical terminology to refer to brachiopods as anything other than "brachiopods". Living brachiopods are few and far between (Prothero, 1998, gives the figure of less than 120 living genera - the photo at the top of this post from Treasures of the Sea shows a cluster of one example, Liothyrella neozelanica) but were one of the dominant life-forms in the Palaeozoic. I must confess ignorance (but a fair amount of curiosity) as to exactly why brachiopods failed to hold onto their position of dominance. Successive mass extinctions (particularly the major die-off at the end of the Permian) seem to have decimated the brachiopods. Perhaps the main clue lies not in the failure of the brachiopods, but in the success of the bivalves - during the Palaeozoic, brachiopods excluded bivalves from all but the more marginal habitats, but bivalves sailed through the end-Permian event relatively unaffected, seemingly to claim the niches the brachiopods had left vacant before the brachiopods were able to reclaim their territory.
The diagram above (from Palaeos) shows the internal anatomy of a brachiopod, and just how different it is from a bivalve. Notably, while the two shells of a bivalve are actually on the left and right side of the animal, the shells of a brachiopod are actually dorsal and ventral. Many brachiopods are attached to the substrate by a pedicle, a fleshy stalk emerging from the back end of the shell through an opening called the delthyrium. The majority of the brachiopod's organs take up very little space in the shell, with most of the space being taken up by the lophophores, pinnate tentacle-like structures that are used to filter food particles out of the water. Because of the lophophore, brachiopods were previously regarded as forming a clade with bryozoans and phoronids (also possessing lophophore-type structures) called Lophophorata. Though the Lophophorata concept was accepted for a great many years, recent analyses have failed to support it. The lophophore in bryozoans is derived embryonically in a decidedly different manner from that of brachiopods and phoronids (Nielsen, 2002 - brachiopods and phoronids still form a clade, the Brachiozoa). Notably, the pterobranchs, a group of small sessile organisms undoubtedly belonging to the deuterostomes, actually have a lophophore-type structure much more like the brachiozoan structure than the bryozoan structure is. Molecular and possibly palaeontological* data place brachiopods somewhere close to the molluscs and annelids, but exact relationships between the three are still unclear.
*Depending on whether the suggested relationship between the brachiopods and the Cambrian halkieriids (e.g. Holmer et al., 2002) holds up.
Rhynchonellata are the major (and the only living) clade of the articulate brachiopods, distinguished from the paraphyletic "inarticulate" brachiopods by the development of proper hinge with sockets and teeth holding together the valves (inarticulate brachiopods use muscles to hold the valves together). Rhynchonellates are distinguished from the Strophomenata, the other (extinct) clade of articulate brachiopods by the absence of a pseudodeltidium (an internal shell plate partially covering the delthyrium) and the presence of a pedicle emerging posteriorly through the delthyrium (Sutton et al., 2005 - ummm, wouldn't these be plesiomorphic characters? Palaeos lists characters of the articulation supporting Rhynchonellata, but unfortunately the source sites linked to appear to be no longer available).
The majority of living rhynchonellates belong to the Terebratulida, including Liothyrella. The Palaeozoic rhynchonellates, of course, showed a much greater diversity, with some eight or so orders (one small living order, the Thecideida, didn't actually appear until during the Mesozoic). One extinct order, the Spiriferida, actually survived the end-Permian event and even made something of a go of it in the Triassic, not fizzing out until sometime in the Jurassic. Spiriferids are probably my favourite group in the brachiopods, going in for a decidedly baroque turn in presentation. As shown in the picture of Mucrospirifer above (from Wikipedia), some spiriferids developed greatly elongated hinge lines, giving them a distinct winged appearance. It is possible that these "wings" supported the brachiopod on soft sediment, allowing the spiriferid to live floating on mud.
Holmer, L. E., C. B. Skovsted & A. Williams. 2002. A stem group brachiopod from the Lower Cambrian: Support for a Micrina (halkieriid) ancestry. Palaeontology 45 (5): 875-882.
Nielsen, C. 2002. The phylogenetic position of Entoprocta, Ectoprocta, Phoronida, and Brachiopoda. Integrative and Comparative Biology 42 (3): 685-691.
Prothero, D. R. 1998. Bringing Fossils to Life: An introduction to paleobiology. WCB McGraw-Hill: Boston.
Sutton, M. D., D. E. G. Briggs, D. J. Siveter & D. J. Siveter. 2005. Silurian brachiopods with soft-tissue preservation. Nature 436 (7053): 1013-1015.
By Christopher Taylor at 12/07/2007 11:09:00 am
I may as well wrap up this series on obscure insect orders I seem to have been doing with one of the most obscure of all - the Zoraptera (for earlier installments on obscure hexapods, see here, here, here and here). Zoraptera are inhabitants of rotting logs in tropical forests (shown above in a photo from The Papua Insects Foundation). A few species range north of the tropics in North America and Asia. Until recently, they were regarded as quite rare, but apparently they have turned out to be not uncommon in suitable habitat. Zoraptera are semi-social, living in colonies of up to a hundred or so individuals.
The name "Zoraptera" means "purely wingless" (the reason for the name should be obvious), and an alternative translation of "zoros" (the same element as in the beginning of "Zoroaster", I believe) explains the occassionally used common name for Zoraptera of "angel insects". There is absolutely no rational justification for calling Zoraptera angels, but the name is just poetic enough that I hope it catches on. It is now known that winged Zoraptera do exist, just not very often. Because rotting logs at just the right stage of decomposition are a temporary resource, zorapterans have an aphid-like life cycle, with blind, wingless individuals breeding and multiplying in their log until resources start running out, at which time winged individuals with eyes start to emerge. These winged individuals are able to leave the doomed colony and seek out a new piece of suitable habitat elsewhere. Notably, the majority of winged dispersers are female - males are quite rare. Female dispersers probably mate with males of their parent colony before dispersing.
Most authors include living species in a single genus, Zorotypus. Kukalová-Peck & Peck (1993) did establish a number of new genera, but as their classification was based on wing characters and could only be applied to a selection of recent taxa (leaving those species for which winged individuals were unknown in a Zorotypus of convenience) it has not been widely accepted. A species from Cretaceous amber has been placed in a distinct genus, Xenozorotypus, with species of the modern genus Zorotypus also known from the same time period (Engel & Grimaldi, 2002).
As I alluded to previously, the phylogenetic relationships of Zoraptera are rather obscure, to say the least. To quote Engel & Grimaldi (2002): "At one time or another Zoraptera has been considered sister to Isoptera (Boudreaux, 1979; Caudell, 1918; Crampton, 1920; Weidner, 1969, 1970), Isoptera + Blattaria (Silvestri, 1913), Paraneoptera (Hennig, 1953, 1969, 1981; Kristensen, 1975), Embiidina (Minet and Bourgoin, 1986; Engel and Grimaldi, 2000; Grimaldi, 2001), Holometabola (Rasnitsyn, 1998), Dermaptera (Carpenter and Wheeler, 1999), Dermaptera + Dictyoptera (Kukalová-Peck and Peck, 1993); basal within Thysanoptera (Karny, 1922) or Psocoptera (Karny, 1932); or unresolved within either basal Neoptera (Kristensen, 1991) or Orthoptera, Phasmida, and Embiidina (Kukalová-Peck, 1991)." At present it is pretty well-accepted that Zoraptera are somewhere within the Polyneoptera, the clade or grade including the cockroaches, crickets, etc., but getting more resolution than this is still difficult. Engel & Grimaldi (2002) favour a relationship to Embioptera, while Terry & Whiting (2005) link them to Dermaptera (earwigs). Rasnitsyn (2002) points out that the characters Engel & Grimaldi used to link Zoraptera to Embioptera are prone to homoplasy, but his own suggestion of a sister-relationship to Holometabola is poorly supported.
Engel, M. S., & D. A. Grimaldi. 2002. The first Mesozoic Zoraptera (Insecta). American Museum Novitates 3362: 1-20.
Kukalová-Peck, J., & S. B. Peck. 1993. Zoraptera wing structures: Evidence for new genera and relationship with the blattoid orders (Insecta: Blattoneoptera). Systematic Entomology 18: 333–350.
Rasnitsyn, A. P. 2002. Cohors Cimiciformes Laicharting, 1781. In History of Insects (A. P. Rasnitsyn & D. L. J. Quicke, eds.) pp. 104-115. Kluwer Academic Publishers: Dordrecht.
Terry, M. D., & M. F. Whiting. 2005. Mantophasmatodea and phylogeny of the lower neopterous insects. Cladistics 21: 240-257.
By Christopher Taylor at 12/07/2007 08:42:00 am
The second edition of Linnaeus' Legacy is up at Laelaps. Take a look to find out what's been happening in the systematic blogosphere over the past month!
January's edition will be hosted by Greg Laden. February we'll be convening at The Other 95%. Hosts for the following months are still needed, so get in touch!
January's edition will be hosted by Greg Laden. February we'll be convening at The Other 95%. Hosts for the following months are still needed, so get in touch!
By Christopher Taylor at 12/05/2007 10:39:00 am
Anderson, D. T. 1992. Structure, function and phylogeny of coral-inhabiting barnacles (Cirripedia, Balanoidea). Zoological Journal of the Linnean Society 106: 277-339.
Barnacles are among the oddest animals on the planet. Genealogically speaking, they're crustaceans, but with such a highly derived morphology that, except for the jointed cirri (actually derived legs), you'd be hard pressed to find an obvious character marking them as such. Much is made of how barnacles spend their lives functionally upside-down (the legs are protruded out to filter food particles from the water, after which they are funneled downwards towards the mouth), their enviable reproductive organs, and how much pain a patch of them can cause while walking below the high-tide mark on a rocky coast. The most familiar barnacles are the rock-inhabiting pyramidal forms, but others seek out different habitats.
Barnacles living on corals have been assigned to three families, the entirely coral-living Pyrgomatidae, the genus Armatobalanus in the Archaeobalanidae and the genus Megabalanus in the Balanidae, but Anderson (1992) agrees with previous authors that the Pyrgomatidae and Armatobalanus form a single clade, with Armatobalanus representing the more ancestral form from which the more specialised Pyrgomatidae originated (the photo at the top of the page, from here, shows the opening of the pyrgomatid Nobia grandis with the cirri extended). Armatobalanus has a wall constructed of six plates as in other families of barnacle, while Pyrgomatidae show a trend towards fusion of the wall plates, with at most four and sometimes a single plate in the wall. The range of variation from more generalised to more specialised forms seen by Charles Darwin during his major revision of the world's barnacles was a significant factor in confirming Darwin's acceptance of the concept of transmutation of species, and the Pyrgomatidae are no exception. Coral-inhabiting barnacles run the gamut, from taxa that are merely resident on the coral and have a fairly typical barnacle morphology such as Armatobalanus, to the derived Hoekia monticulariae with fused opercular plates, vestigial cirri and enlarged mouthparts that feeds directly on the coral overgrowing it.
The greatest threat to any coral-living animal is being overgrown by the coral itself. In Armatobalanus, this is prevented using purely mechanistic means - as the cirri are extended from the aperture, they actively scrape away any overgrowing coral, and enlarged maxillipeds that also protrude from the aperture flick away the resulting debris. In the Pyrgomatidae, a frill has developed that protrudes from the aperture when open on either side of the cirri, and probably secretes a growth inhibitor that excludes the coral (the presence of some sort of chemical defense is indicated by the fact that dead barnacles are rapidly overgrown). Some species of the less derived pyrgomatid genus Cantellius, while possessing the apertural frill, also retain the teeth on the cirri and enlarged maxillipeds of Armatobalanus species. More derived pyrgomatid species show a trend towards reduction in size of the aperture, which Anderson (1992) suggests may be because that reduces the size of the perimeter the barnacle needs to keep clear of coral. The downside of aperture reduction is that it requires some degree of reduction in the size of the cirral fan, and hence reduces feeding efficiency. It has long been suggested that at least some pyrgomatids may compensate for the reduced feeding ability through some degree of parasitism from the host coral, either through tissue feeding or absorption of dissolved nutrients. While many species do show a trend towards weakening of or the development of pores in the basal shell or membrane separating the barnacle from its host (and this basis is completely lost in Hoekia), direct evidence for parasitism in genera other than Hoekia is slight. No evidence of nutrient transfer was found in a study of Newmania milleporum, but Anderson (1992) points out that Newmania is one of the more actively-feeding species, without a reduced basis, so is not one of the most likely candidates for parasitism anyway.
On the basis of morphology, Anderson (1992) suggested a phylogeny for the pyrgomatid subfamily Pyrgomatinae that placed the derived genera in three groups arising independently from the basal Cantellius, which was itself derived from Armatobalanus or an Armatobalanus-like ancestor. However, this phylogeny was not supported by the more recent molecular study by Simon-Blecher et al. (2007). In their phylogeny (shown above, from the paper - the drawings to the right of each taxon represent the arrangement of wall plates and the shape of the opercular plates), Armatobalanus is actually nested within the pyrgomatids (and one "pyrgomatid" genus, Wanella, seems to actually be a convergent member of the Balanidae). If the phylogeny of Simon-Blecher et al. (2007) is correct, then there appears to have been a fair degree of homoplasy in the fusion of the wall plates from the ancestral six retained in Armatobalanus. The most interesting possibility suggested to me by the molecular phylogeny, however, is that the mechanistic method of coral exclusion of Armatobalanus, rather than being ancestral, may actually be derived relative to the chemical inhibition method. Cantellius, the genus Anderson (1992) suggested retained relictual features of the mechanistic method, is sister in Simon-Blecher et al.'s (2007) tree to Armatobalanus, adding more credility to the idea that we should reverse our ideas of ancestral vs. derived.
Simon-Blecher, N., D. Huchon & Y. Achituv. 2007. Phylogeny of coral-inhabiting barnacles (Cirripedia; Thoracica; Pyrgomatidae) based on 12S, 16S and 18S rDNA analysis. Molecular Phylogenetics and Evolution 44 (3): 1333-1341.
By Christopher Taylor at 12/03/2007 12:01:00 pm
The copepods are a widespread group of aquatic crustaceans, another one of those groups of minute animals that are all around us, yet attract little attention because of their tiny size. Thousands of copepod species have been described from every imaginable habitat involving a certain degree of water - thousands more doubtless remain to be described.
In the tiny world of copepods, members of the family Aegisthidae are relative giants, attaining massive sizes of more than 1.5mm in length (in contrast, the type specimen of their sister taxon, Romete bulbiseta, measures a mere 360 microns). Aegisthidae are one of the more basal members of the Harpacticoida, one of the largest orders of copepods. Basal members of the order are fusiform, but many of the more derived infaunal species have a more vermiform shape. Some three thousand harpacticoid species have been named to date, and they are second only to nematodes in abundance in the meiofauna (Seifried, 2003).
The relatively large size of the Aegisthidae is probably connected to their different lifestyle from other harpacticoids - rather than being epibenthic (living on the surface of the substrate) or infaunal (burrowing within the substrate), many Aegisthidae are hyperbenthic - that is, they live in the water column just above the surface of the substrate (there is a bit of confusion about correct terminology - other authors refer to "demersal zooplankton" or "benthopelagic plankton". Funnily enough, the choice of terminology is generally connected to which marine setting, whether tropical, temperate or deep sea, the author is mostly working with - Mees & Jones, 1997). There is also a tendency to lengthen the body shape, particularly the caudal rami, two spine-like extensions from the posterior end of the abdomen (the image of Aegisthus at top left of this post, from here, shows just how incredibly long the rami can get). A few species of Aegisthidae have gone the whole pelagic hog and become genuine members of the upper zooplankton, some of the relatively few harpacticoids (members of only three families) to have done so.
I had intended to centre this post on just one of the aegisthid subfamilies, the Cerviniopsinae. It is worth noting that Aegisthidae once referred to a much smaller collection of species, the current subfamily Aegisthinae (including the holoplanktic species). However, Seifried & Schminke (2003) argued that the 'Aegisthidae' of previous authors represented a derived subgroup of the previous family Cerviniidae, rendering the latter paraphyletic and calling for its sinking. The 'cerviniid' subfamily Cerviniopsinae was recognised as probably also paraphyletic with regard to Aegisthinae, and in particular a connection was suggested to the 'cerviniopsine' genus Pontostratiotes. Nevertheless, Seifried & Schminke did not formally remove the Cerviniopsinae from their classification, retaining it as a provisional grouping pending a proper phylogenetic analysis of the Aegisthidae. Most of the Cerviniopsinae do not appear to have been dealt with since Lang's major monograph of the harpacticoids back in 1948. Members of the Aegithinae share at least one distinguishing feature of the Cerviniopsinae, having the caudal furci opposed to each other rather than divergent as in the Cerviniinae (Montagna, 1979). Members of the Aegisthinae show a tendency to reduction of the mandibles in the males, with the adult males of some species such as Andromastax muricatus and Aegisthus mucronatus being entirely non-feeding.
Mees, J., & M. B. Jones. 1997. The hyperbenthos. Oceanogr. Mar. Biol. Ann. Rev. 35: 221-255.
Montagna, P. A. 1979. Cervinia langi n. sp. and Pseudocervinia magna (Copepoda, Harpacticoida) from the Beaufort Sea (Alaska, USA). Transactions of the American Microscopical Society 98 (1): 77-88.
Seifried, S. 2003. Phylogeny of Harpacticoida (Copepoda): Revision of “Maxillipedasphalea” and Exanechentera. Cuvillier Verlag: Göttingen.
Seifried, S., & H. K. Schminke. 2003. Phylogenetic relationships at the base of Oligoarthra (Copepoda, Harpacticoida) with a new species as the cornerstone. Organisms, Diversity and Evolution 3: 13-37.