More From the "They Don't Write Papers Like They Used To" Files

But before that, a couple of other things:

Recent Carnivals - Berry Go Round is here, Circus of the Spineless is here.

Also recently, the Open Laboratory 2008 collection of some of the year's best online science writing is now available. In the interests of disclosing all interests (naturally), yours truly has a piece featured in this publication - on citrus fruit. Anybody who has heard me commenting on my poor knowledge and outright terror of botany will know that this is a Very Funny Thing.

On to the main point of the post, which will not be anything I'm writing at all...

Recently, I was reading a paper from 1866 by a Dr H. Dohrn with the unprepossessing title of "Synopsis of the birds of Ilha do Principe, with some remarks on their habits and descriptions of new species" (Proceedings of the Zoological Society of London 1866: 324-332). Principe, for those who don't know it, is a part of the country of Sao Thomé and Principe in west-central Africa. This is the second paragraph of that publiction:

It seems to me that the most remarkable feature in the fauna of Ilha do Principe is that not a single bird of prey exists on the island, whilst they are abundant on the two other islands and on the nearest part of the continent. I saw hundreds of Milvus parasitus in San Thomé; Gypohierax angolensis and some other species are not uncommon in Fernando Po; but the whole tribe avoids Principe. The inhabitants of the latter place and of San Thomé assert that there is a deadly hatred between the Grey Parrots (Psittacus erythacus) of Principe and the Kites of San Thomé, and that, if ever a Milvus visits the neighbouring island, hundreds of Parrots fall upon him and kill him, and that the Kites take revenge if perchance a Parrot should venture a trip to their kingdom. There must be some family reason for this strange degree of enmity, for they seem to live in tolerable peace together on the coast.

You will probably not be surprised to hear that I was somewhat taken aback by this - even allowing for the different time period, it seemed a rather credulous account. But as I read further, I realised that Dohrn was employing something that is a little alien to modern academic writing: irony.

To demonstrate my point, here are my other favourite passages from Dohrn:

On a species of drongo:

The native name is "Maria Palu, feiticeira" (translated, Maria Palu, the sorceress). The bird is black, with red eyes; seems very indolent in daytime, and shows a great ability in the imitation of some other birds' voices. Of course there must be some "feiticeira" to it: therefore, sitting on the roof of a house and singing in its melancholy manner, it prophecies the death of one of the inhabitants; and this, of course, takes place, but often a long time after this prophecy.

On the bald ibis:

Soon after my arrival on the island I was informed by some natives that there was a very remarkable bird in the island called "Corvão." One told me that it was a kind of raven with splendid metallic wings; another described the bird "with the head of an owl and the feet of a duck, climbing up and down trees;" and others gave me other extravagant descriptions of it; but all of them agreed that the bird lived in almost inaccessible rocky and wooded localities of the southern district, and that if ever a specimen passed over the town it was a bad omen for the white inhabitants, who in such case were exposed to heavy disease or death. Of course I was very curious to see this species, and settled for a fortnight in a negro's hut in those desert parts of the island*. Whoever has visited those large tropical forests knows the difficulty of proceeding there. I enjoyed the special favour of heaven in arriving there when the rains set in a month before they usually do, and it was very hard work to run after these birds. I saw them daily at great distances, and heard them crowing like a Raven; but as soon as I entered the forests the monkeys made so much noise, barking and howling, as to alarm all the animals in the neighbourhood. Thus I was finally very glad when one of my native hunters appeared with a female specimen of the Corvão, which turned out to be Geronticus olivaceus.

*I think in this case "desert" means "deserted", not "arid".

Les is More

The avialan theropod previously referred to here as "Les" has now made its official, honest-to-goodness debut in the latest issue of Nature, and I can now reveal the proper name for Les - Epidexipteryx hui (the genus name means "display feather" and refers to the fact that the feathers preserved for Epidexipteryx appear to have been used for display rather than flight). It's a pretty fossil, but Nature has pulled its usual frustrating trick of giving us just enough information to whet the appetite, and leaving us howling frustratedly for more information...

Reconstruction of Epidexipteryx hui above taken from The Loom.

Let's Have Less of Les

Tom Holtz of the University of Maryland has confirmed via the Dinosaur Mailing List that the fossil animal introduced in the last post as Les is a snafu. The authors of Les intended for their manuscript to be submitted online to Nature, and its arrival on Nature Precedings was a mistake. There is every possibility that the name given to Les in the manuscript will change before publication (pity, I rather liked the name they'd given), and the reviewers may actually recommend that the authors do just that. It is not uncommon practice for reviewers to recommend that authors not use names that are leaked to the public in some way before publication - I suppose to distance the finished product from the rumour mill, though personally I think it probably confuses things even more.

Still, the very fact that such slips can happen so easily just reinforces everything I said in the last post about the need to discuss how the internet affects our concepts of publication, and whether or not we need to adjust our concepts of how to determine priority accordingly.

A New Stem-Bird and Publication in the Digital Age

Scansoriopteryx heilmanni, as reconstructed by Stacey Burgess.

First off, notification of the focus of this post came via the Dinosaur Mailing List.

It is almost a truism that the internet has changed the face of scientific publishing. Online versions of journals have become the first port of call for many, if not most, researchers. The paper reprint has become an endangered species, and articles are exchanged via e-mail as pdfs. Online-based journals such as BMC Biology and the PLoS collection have abandoned the standard journal format with articles collected into issues, and release articles as and when they become available. Even among those journals that still release regular issues, many have begun offering advance online releases of upcoming articles. For most branches of science, these advances are mostly all for the good. Good science, after all, is largely dependent on access to information, and there is much to be said for allowing the dissemination of new information as quickly and easily as possible. However, at least one branch of science, taxonomy, remains firmly attached to the printed page, and has good reasons for doing so.

As alluded to here before, taxonomy differs from other sciences in that it provides the means for communication between biologists working in other disciplines as well as being a target of investigation in its own right. In order to facilitate communication, it makes sense that (a) the taxonomic system should be as stable as possible*, and (b) when conflicting taxonomies do arise, then the means for determining the correct nomenclature to use should be as simple and automatic as possible. It is to satisfy this second requirement that taxonomic systems employ the principle of priority - if two separate names exist for the same taxon, then the correct name to use is the one that was published first.

*Though, as with governments, "stable" in this context does not necessarily mean "unchanging". Rather, it means "not prone to change without proper cause".


Scansoriopteryx again, this time by Matthew Martyniuk.

Of course, saying that the first name to be published is correct immediately raises the question of what counts as publication. The International Code of Zoological Nomenclature (Article 8) requires that a published work must be issued in a permanent format, and must be generally made available upon publication. These are pretty broad criteria, but any work (and any new names within) cannot be considered published until they are met. The date at which these criteria are met becomes the official date of publication. Release of an article online (such as in a pre-print) does not count as publication in this sense because a webpage is not permanent. While a book requires little or no attention once it has been accessed in a library and can sit there more or less indefinitely*, a webpage requires continual upkeep to remain available. The ICZN does allow a name to be published online if some form of permanent copy (such as a print-out or CD) of the webpage is deposited in a number of major public libraries (such as the American Library of Congress). As far as I know, the Botanical Code still insists on printed publication.

*Okay, theoretically a book may be at risk of decaying after a few hundred years, but that's still pretty permanent compared to a website.

In June last year, the Nature group launched Nature Precedings, an online repository for preliminary findings and manuscripts, allowing researchers to share data of interest that might or might not be sufficient for an eventual completed paper, obtain feedback on said preliminaries that might improve the final manuscript, and just generally keep other researchers informed on what was going on. Entries on Nature Precedings are not peer-reviewed before becoming available, and are generally not regarded as completed publications. A few days ago, a new entry was loaded on Nature Precedings by Zhang et al. describing a decidedly interesting new dinosaur species, complete with attached name. Officially, this taxon is not yet published. Because of the interest that surrounds any new dinosaur discovery, you can bet your ass that that won't stand in the way of its becoming widely known.


The new scansoriopterygid, which I'm calling Les. Figure from Zhang et al.

As I said, there's a name attached to the new taxon. It's a very nice name, too - kind of rolls off the tongue. But because I'd rather avoid using an unpublished taxon name, I'm keeping shtum (of course, click on the link and you'll find the name right away, so my protest is really pretty pointless). Because the new species is a member of the family Scansoriopterygidae, I'm going to call it LES (standing for "Looks like Epidendrosaurus or Scansoriopteryx"). Les was a small bird-like theropod about the size of a pigeon, and represented by a very nice nearly-complete skeleton, complete with preserved feathers including a tail of four long ribbon-like feathers that were about as long as the rest of the animal. Phylogenetically, Zhang et al. position Les as more closely related to modern birds than the dromaeosaurs (Velociraptor et al.) but less closely related than Archaeopteryx. Les is exactly the sort of thing that might eventually be published in Nature, and its appearance in Nature Precedings gives the impression of leading into doing so.

The family Les belongs to, Scansoriopterygidae, has become something of a poster child for the issues surrounding online publication. Two genera have previously been named for scansoriopterygids, Scansoriopteryx and Epidendrosaurus, but most researchers suspect that these two names refer to the same animal. Unfortunately, determining which of the two names has priority is not a straightforward question, as discussed by Harris (2004). Both names were published in 2002, but the book naming Scansoriopteryx was probably less widely read than the journal naming Epidendrosaurus. Epidendrosaurus appeared in an online preprint on the 21 August, but the printed version didn't appear until 30 September. The exact date of publication of Scansoriopteryx is a little debatable, but it seems to have become available by 2 September - after the name Epidendrosaurus became widely publicised online, but before the official publication of Epidendrosaurus. Technically, Scansoriopteryx has priority, even though Epidendrosaurus was the name that became known to the public first.

The lesson from cases such as Scansoriopteryx is that the time has well and truly arrived for us to re-evaluate what it means for a name to be "published" in the digital age. In the past, the first a public would generally hear of a manuscript and its contents was when the finished publication arrived in all its official glory. Now, as demonstrated by Les, it may be possible for a manuscript to appear online as a rough draft, as a polished pre-print, as the final official product. Should these early appearances be regarded as valid publications? When the manuscript first appears, or only as it approaches its final form? The initial format for publication of Epidendrosaurus may not have been permanent, but should we regard the later appearance of a permanent printed edition as having validated that initial appearance? The rules of the game are changing. It is time to decide whether we should keep playing.

REFERENCES

Harris, J. D. 2004. 'Published works' in the electronic age: recommended amendments to Articles 8 and 9 of the Code. Bulletin of Zoological Nomenclature 61 (3): 138-148.

Bird Evolution - Problems with Science

Hackett, S. J., R. T. Kimball, S. Reddy, R. C. K. Bowie, E. L. Braun, M. J. Braun, J. L. Chojnowski, W. A. Cox, K.-L. Han, J. Harshman, C. J. Huddleston, B. D. Marks, K. J. Miglia, W. S. Moore, F. H. Sheldon, D. W. Steadman, C. C. Witt & T. Yuri. 2008. A phylogenomic study of birds reveals their evolutionary history. Science 320: 1763-1768.

I'm afraid I'm going to be descending into cattiness for a moment later. I apologise in advance for any unwarranted snarkiness.

A paper (citation above) has appeared in today's edition of Science that adds to the ongoing debate on bird phylogeny. It is a fairly significant paper, giving the results of the largest molecular phylogenetic analysis to date for birds. As such, it largely supersedes the previous front-runner, the analysis of Ericson et al. (2006). However, most of the results of Hackett et al. (2008) are largely congruent with those from Ericson et al. (2006). So I'm a little bemused to read Chuck Hagner commenting that "What wasn’t expected was an apparent sister relationship between Passeriformes and Psittaciformes" and expressing surprise that Falconidae should cluster with that clade instead of with Accipitridae, when both these results had been reported in the 2006 paper. What is significant is that both these studies, conducted independently (no shared authors), found such similar results. Both studies (and the earlier Fain & Houde, 2004) found the same six major clades - Palaeognathae (ratites and tinamous), Galloanserae (gamebirds and waterfowl), Metaves (I'll explain in a minute), the "higher water-birds and allies" clade (including 'Ciconiiformes' and 'Pelecaniformes' intermixed), Charadriiformes and the "higher land-birds" (Passeriformes, Piciformes, Coraciiformes and allies).


Bird phylogeny as recovered by Hackett et al. (2008).

Metaves is one of the most controversial groupings of birds to have been proposed in recent years. It first made an appearance in a 2004 paper by Fain and Houde published in the journal Evolution. These authors coined the name Metaves for a clade containing nightjars, swifts and hummingbirds, pigeons and doves, sunbitterns, the kagu, mesites, tropicbirds and the hoatzin that was well-supported in an analysis of the β-fibrinogen gene. This clade was then completely unexpected - perviously, its members had been scattered among an assortment of other bird orders, and the only thing a number of them had previously had in common was that they had always looked a little out of place. In a message forwarded to the DML shortly after the publication of the 2004 paper, Peter Houde commented that the results had been so heterodox that it had been very difficult to get them published. The Charadriiformes, higher land-birds and higher water-birds together formed a clade that Fain and Houde dubbed "Coronaves". The Fain and Houde analysis did resolve the Charadriiformes and higher water-birds, but support was not great.

Ericson et al. (2006) increased the number of genes analysed to five, and again found the Metaves-Coronaves division of Fain & Houde (2004). They were also better able to resolve relationships within the major clades. However, the support for Metaves was completely reliant on the inclusion of the β-fibrinogen gene. If this gene was left out of the analysis, the clade collapsed.

Not too long after Ericson et al. (2006), a counter-sally from the morphological fort appeared in the form of the long-awaited Livezey & Zusi (2007) analysis. Using an awe-inspiring 2954 characters over 150 taxa, this morphological über-analysis bravely fought off the molecular novelties and called stridently for a return to more traditional relationships.

It is into this clash between the molecular data of Ericson et al. (2006) and the morphological data of Livezey & Zusi (2007) that Hackett et al. (2008) make their entrance. Hackett et al. increase the number of analysed genes to 19, and once again recover the much-maligned Metaves. Once again, though, the presence of this clade is dependent solely on the β-fibrinogen gene. The hoatzin abandons the Metaves and attaches itself to the base of the higher water-bird clade. I'm inclined to describe this as unsurprisingly surprising - once again, Opisthocomus is just being a prick. There seems to be a visible trail of respectability here - four years ago, Metaves had to fight its way for recognition in a respectable journal. With the publication of a paper supporting it in Science, it seems to have become a respectable hypothesis.

And that, really, is the source of my irritation. Nature and Science are widely regarded as the ultimate science journals, but it's difficult to escape the observation that many papers that appear in the two are, well, kind of crap. This is not the fault of the contributing authors, but results from the severe space restrictions on articles in these journals. At five very densely-written pages, Hackett et al. is a fairly long paper for Science, but the reader is left frustrated by the need to know about stuff that the authors were evidently forced to leave out. What happens when the analysis parameters change? If a given clade is collapsed, how does this affect the rest of the tree? Some of this is alluded to in the article, but there simply isn't the time for it to be explored properly. And was it lack of space that caused the authors to write clangers such as "flighted tinamous arose within the flightless Struthioniformes", which sounds to be suggesting that tinamous evolved or regained flight independently of other birds, rather than the far more likely scenario that flight was lost multiple times within the ratites? Nature and Science papers have been referred to as "extended abstracts" Sometimes, no matter how extended, an abstract just doesn't substitute for a paper.

Don't get me wrong, this is a very significant paper, and one that will provide a base-line for many future studies. It doesn't completely overthrow previous studies, but in the end that is exactly what is so fantastic about it - not that the results are completely unexpected, but that as more and more data is added, we can say more and more about the picture that has been developing over the past few years.

REFERENCES

Ericson, P. G. P., C. L. Anderson, T. Britton, A. Elzanowski, U. S. Johansson, M. Källersjö, J. I. Ohlson, T. J. Parsons, D. Zuccon & G. Mayr. 2006. Diversification of Neoaves: integration of molecular sequence data and fossils. Biology Letters 2 (4): 543-547.

Fain, M. G., & P. Houde. 2004. Parallel radiations in the primary clades of birds. Evolution 58 (11): 2558-2573.

Livezey, B. C., & R. L. Zusi. 2007. Higher-order phylogeny of modern birds (Theropoda, Aves: Neornithes) based on comparative anatomy. II. Analysis and discussion. Zoological Journal of the Linnean Society 149 (1): 1-95.

How Irritable is This Bird?

Jackass penguin (Spheniscus demersus). Photo by Tuxette.

It's definitely intriguing how the meanings of words can change over the years. A Blog Around the Clock recently presented a quote that claimed that Charles II described the newly-built St Paul's Cathedral as "awful, pompous and artificial". This was entirely complimentary - "awful" indicates something that inspires awe, "pompous" roughly means "majestic", while "artificial" means that it indicated a great deal of artifice on the part of its builder - and "artifice" would have meant "technical or artistic skill", having not yet gained its current connotation of duplicity and deception. "Automaton" is another word that has changed significantly in meaning. It literally means "self-moving", and so when it was first coined would have indicated the independent, undirected movement and action of the subject - almost the complete opposite of its current usage.

I bring up those examples to segue into another change in meaning that I came across yesterday. I happen to have in front of me a copy of the Proceedings of the Zoological Society of London for 1866, in which (amongst other things) W. Lilljeborg presented a revised classification for birds. In explaining the principles on which he based his classification, Professor Lilljeborg notes:

Irritability seems to us to be the most distinguishing character for birds, and this should consequently be taken into consideration more than others with regard to their classification.

Canada goose (Branta canadensis). Photo by George K.

I'm sorry? You're classifying birds according to how irritable they are? Fortunately, Lilljeborg further explains, "We do not by irritability mean the muscular strength alone, but vivacity and activity generally". Lilljeborg was basing his classification on a principle that evolution had proceeded from less derived, more sluggish forms to more derived and accomplished forms. All horribly Scala Naturae-based, of course, and more than a little inaccurate in some regards:

The swimmers seem to us the lowest, from their showing a tendency to the lowest form of vertebrated animals - the fish-form. In the [penguins], where the wings resemble fins, and where they, as in all other diving birds, serve as such, we have this form most strongly designated. The heavy, clumsy structure, with small wings and short legs, also makes them generally less active than other birds, and shows a lower development of the type of bird.

Southern yellow-billed hornbill (Tockus leucomelas). Photo by Tuxette.

A description obviously heavily biased by observations of penguins almost solely on land, not in the water where they are far more adept. I also had to snicker somewhat at Lilljeborg's complaint about the previous tradition of placing the birds of prey (rather than the passerines he favoured) at the "summit" of avian evolution:

A system that places the dirty vultures highest, does not seem to us to indicate a correct idea of the nature of birds.

Great blue heron (Ardea herodias). Photo by tofrg.

Lest I give you too negative impression of Lilljeborg's skills as a systematist, his final classification stands up fairly well by the standards of the time. The classification itself was generally based on good anatomy - the philosophical considerations mostly affected what order he listed things in. Still, I couldn't read that section on "irritability" without getting the mental image of Professor Lilljeborg, his fingers heavily bandaged, making his way down a row of birds sitting in cages, poking each one in turn with a chopstick and seeing how long it took to snap back. One suspects he probably left the eagle until last.

REFERENCES

Lilljeborg, W. 1866. Outlines of a systematic review of the class of birds. Proceedings of the Zoological Society of London 1866: 5-20.

A Frustrating Giant Bird

Darren Naish in a recent post on his most excellent Tetrapod Zoology blog on a completely different subject mentioned the giant fossil bird Eremopezus, which inspired me to look it up (I was nearly inspired to change subject by watching a bagmoth in the lab here sealing itself into its bag in preparation for pupating, but another time, perhaps...)

Eremopezus is known from leg bones from the upper Eocene of the Fayum of Egypt. The most recent review is by Rasmussen et al. (2001), but it was first described in 1904. Lambrecht later divided the then-available material into two genera, Eremopezus Andrews 1904 and Stromeria Lambrecht 1929, but there is little significant difference between material assigned to the two and they are now regarded as synonymous.

Being a giant landbird, Eremopezus was originally thought to be related to modern giant landbirds, the ratites. Ratites are a group of flightless birds distributed between the southern continents - the ostrich (Africa), rheas (South America), emu, cassowaries (Australia), moa and kiwis (New Zealand). Arguments have run back and forth about whether the ratites are monophyletic, or have arisen independently from different ancestors. Recent molecular phylogenies have been pretty much unanimous that the ratites are indeed monophyletic, and together with the flighted tinamous (Tinamidae) are the sister group to the remaining modern birds. On the basis of a prominent ridge on the tarsometatarsus, Lambrecht (1933) suggested that Eremopezus was related to the elephant birds (Aepyornithidae) of Madagascar.

The problem is that this is simply not very significant evidence, as pointed out by Rasmussen et al. (2001). Large flightless birds show a great deal of similarity in the form of the leg bones, due to similar functional requirements. The flightless carnivorous bird Diatryma has hindlimb bones indistinguishable from those of ratites, despite being more closely related to the modern Anseriformes (ducks and geese). Rasmussen et al. concluded that Eremopezus could not be reliably associated with any other known group of birds.

To add to this, Eremopezus showed a number of distinct features all of its own. It appears to have been a fairly lightly-built bird, but slightly larger than a cassowary or rhea. The distal end of the tarsometatarsus is markedly flattened dorsoventrally, and the trochleae (and hence the toes) are quite widely splayed (an attachment scar indicating the presence of a hallux - the rear-pointing toe - is present, but this was probably small as an adaptation for terrestriality). The trochleae on either side have relatively light grooves, suggesting that the toes were quite mobile. The modern birds with the most similar morphologies are Sagittarius serpentarius (secretarybird) and Balaeniceps rex (shoebill). Both these birds use their feet for manipulation - Sagittarius is a ground predator that catches prey with its feet, while Balaeniceps uses its feet to grasp floating vegetation in swampy habitats. The Fayum of the Eocene also appears to have been a quite swampy habitat, but the appeal of a gigantic secretarybird is not to be denied. In the meantime, we simply have to wait on further remains to turn up before we can say more on the subject.