Clouded leopards and the species problem

January 25, 2011 • 10:48 am

by Greg Mayer

Alert WEIT-blog reader Dominic has drawn my attention to a not yet published study of clouded leopards, that I’d seen mentioned by the BBC, but I had not seen the actual paper (well, actually, nobody has seen the actual paper— more below on this).

Clouded leopard by Vearl Brown, from Wikipedia.

There are two issues here, both of which we’ve considered before here at WEIT. First is the species concept issue, which both Jerry and I mentioned recently (links to Jerry’s posts in mine). The second is a scientific nomenclature issue, one that arose in the infamous Darwinius case.

The species concept issue also comes in two parts. First, are the mainland clouded leopard (Neofelis nebulosa) and the insular clouded leopard (Neofelis diardi) distinct species? And, second, among the insular clouded leopards, are the Bornean and Sumatran populations distinct? The first issue was the focus of two papers in 2006 which raised the insular leopards to full species status. Normally, the raising of insular forms to full species status on the basis of being different from the mainland form raises a warning flag for me, but there is an additional consideration which I think in this case supports the raising to full species status. This is that the islands of Borneo and Sumatra are on the Sunda Shelf, and thus were connected to the mainland as recently as about 10,000 years ago (see Harold Voris’s superb series of paleo-bathymetric maps of the Sunda Shelf for details). So, the insular and mainland forms were in contact very recently, and one good explanation for why this contact would not have led to an erosion of the genetic differences between them is that they were reproductively isolated (i.e., different species). There are other possible interpretations, but the recent contact combined with observed differences certainly makes the 2-species taxonomy reasonable.

The new, unpublished, paper argues not for a new species, but for dividing the insular form into two subspecies, one from Borneo and one from Sumatra. (A subspecies is recognized when there is a particular pattern of geographic variation within a species, namely that there is a geographic segment of the species’ range within which individuals can be distinguished from individuals from other parts of the range. Basically, if you can tell where an individual is from by the way it looks, or, if you tell me where the individual is from, I can tell you what it looks like, then you can name a subspecies.) This seems perfectly reasonable to me.

The problem is that they describe a new subspecies in the paper (rather than reviving a previously described one), but they have also posted a pre-print online and allowed press coverage. Online posting does not constitute publication in the formal sense, and their paper will soon be published on paper. But by generating press coverage (the BBC has included the new name in its coverage) and posting online, they increase the chance that the name will be formally published before their paper appears in print, either accidentally, or on purpose by an unscrupulous individual wanting to steal credit for their work (it does happen). This was part of the problem with Darwinius: the name Darwinius was bandied about before the name was published.

The authors are actually compounding a problem they created for themselves earlier: they published the new name in 2007 (I have not seen this paper), but now consider their proposal at the time nomenclaturally defective, and the name not nomenclaturally available from that publication. (The technical term for what they now regard their 2007 effort is a nomen nudum: a nude name, i.e. a name without a proper description accompanying it, and thus not available for use as a scientific name). The nomenclature of this name could be confused. I hope their paper appears soon.

One thing highlighted by this paper that I want to unreservedly endorse is the use of camera traps for the study of elusive large mammals. These traps have helped with studies of a number of species, including several big cats: jaguars (including Arizona jaguars), Saharan cheetahs, Asiatic cheetahs, tigers, as well as clouded leopards. The BBC, NYT, and other media often highlight the results of these studies. Recently, camera traps revealed an unexpected high-altitude population of tigers in Bhutan, in a valley where three big cats– leopard, snow leopard, and tiger– all live together.

Buckley-Beason, V.A. et al. 2006. Molecular evidence for species-level distinctions in clouded leopards. Current Biology 16:2371-2376. (pdf)

Kitchener, A.C., M.A. Beaumont, and D. Richardson. 2006. Geographical variation in the clouded leopard, Neofelis nebulosa, reveals two species. Current Biology 16:2377-2383. (pdf)

Wilting, A., V.A. Buckley-Beason, H. Feldhaar, J. Gadau,  S.J. O’Brien, and K.E. Linsenmair. 2007. Clouded leopard phylogeny revisited: support for species recognition and population division between Borneo and Sumatra. Front. Zool. 4:15. (not seen)

Wilting, A., P. Christiansen, A.C. Kitchener, Y.J.M. Kemp, L. Ambu, and J.Fickel. 2011. Geographical variation in and evolutionary history of the Sunda clouded leopard (Neofelis diardi) (Mammalia: Carnivora: Felidae) with the description of a new subspecies from Borneo. Molecular Phylogenetics and Evolution in press. (pdf)

New australopithecine described

April 8, 2010 • 11:26 am

by Greg Mayer

Lee Berger of the University of the Witwatersrand and several colleagues will be describing a new species of Australopithecus, A. sediba, from 1.78 to 1.95 million-year-old deposits in South Africa, in tomorrow’s issue of Science. The issue will also have a geological article on the find by Paul H.G.M. Dirks of James Cook University, Queensland, and colleagues, and a news item, all available now at Science‘s website (plus a podcast and video). The description is based on two partial skeletons, including a well preserved juvenile skull, most of the right arm and shoulder girdle, parts of the hip and leg, and various other bits.

Skull of juvenile Australopithecus sediba. Image from University of the Witwatersrand.

The new species has a long arm, but the pelvis and leg indicate that it was bipedal (i.e. it could both climb and walk upright). The general evolutionary conclusion the authors draw is the mosaic nature of the origin of Homo features: some Homo-like characters evolved before others, e.g. bipedality preceding cranial enlargement. They find specific features linking the new species to Homo, and posit it to be intermediate between earlier australopithecines and Homo:

The age and overall morphology of Au. sediba imply that it is most likely descended from Au. africanus, and appears more derived toward Homo than do Au. afarensis, Au. garhi, and Au. africanus.

Something I rather liked about the paper is that it is quite data rich, having tables of comparison of traits and measurements of the new find and several other fossil hominids. Such data-richness is unusual for papers in Science, which prefers short papers, with data often being relegated to electronic appendices or other papers; the Berger et al. paper is an unusual ten pages long.

The news has already reached media websites (e.g. the New York Times, the BBC and the Telegraph). Unlike the case of Darwinius masillae, however, in which premature press coverage, which included the name and its diagnostic characters, and web posting of the description, led to questions about the proper authorship and publication of the name, the authors and journalists in this case have done everything right. The news accounts are appearing coincident with the name being published (i.e. printed on paper), not prior to its publication. (The newspaper pieces linked to above are online now, but they won’t be published in the sense of the International Code of Zoological Nomenclature until tomorrow, when the scientific paper itself will be published.) There will thus be no questions about the publication of the name; the authors have made sure that, as the ICZN recommends, Australopithecus sediba is “self-evidently published within the meaning of the Code” (ICZN, Rec. 8B)

An iguana appetizer

January 16, 2010 • 1:07 am

by Greg Mayer

No, it’s not a reptilian hors d’oeuvre. It’s pictures of a Galapagos land iguana, Conolophus subcristatus, to whet your appetites for those Jerry will have when he gets back. I toured the Galapagos 20 years ago, and took loads of pictures, but they’re Kodachromes (which I haven’t scanned), so the pictures of our saurian friend below are from my colleague and fellow evolutionary biologist Joe Balsano, who visisted in 2007, and then kindly regaled my Darwin class with tales and pictures of his adventure. (More Galapagos reptile photos, at the Galapagos Conservancy, here.)

The Galapagos land iguana, Conolophus subcristatus (Joe Balsano).

The first link above for the Galapagos land iguana, from the Galapagos Conservation Trust (the UK companion to the US-based Galapagos Conservancy) is slightly out of date when it says there are two species of Galapagos land iguana: there are three. The common, or just Galapagos, land iguana, Conolophus subcristatus, is shown above. The Barrington land iguana, C. pallidus, occurs only on the island of Santa Fe (also known as Barrington). The two species differ fairly subtly in color and scalation (pallidus being less colorful, with a more distinctive crest of spines; see the original description by Edmund Heller here [go to Proceedings of the Washington Academy of Sciences in the left sidebar], and the classic paper by van Denburgh and Slevin on Galapagos iguanid lizards from the California Academy Expedition here [go to Proceedings-California Academy of Sciences 4th series in the left sidebar]). These subtle differences are the sort of differences between allopatric populations (i.e., populations inhabiting distinct, nonoverlapping, geographic areas) that can lead to long and inconclusive arguments as to whether the populations should be recognized as species, or subspecies, or not named at all. These arguments are a common, and not at all unexpected, issue when dealing with organisms living on islands. (The evolutionary process issues involved, although not the taxonomic issues, are dealt with comprehensively in Jerry’s and Allen Orr’s Speciation.) But the newly discovered species the pink land iguana of Volcan Wolf on Isla Isabela (Albemarle), Conolophus marthae, is not one of these wishy-washy, is-it or is-it-not-a-species, cases: it’s a new species, alright.

The pink land iguana, Conolophus marthae. From Gentile, G., et al. 2009. An overlooked pink species of land iguana in the Galápagos. Proceedings of the National Academy of Sciences 106:507-511.

It is amply distinct, both morphologically and genetically, from the other two species, including in coloration and form of the nuchal crest, as you can see from the pictures above. But, more importantly, it is also sympatric (i.e., living together in the same place) with the common land iguana. This is important because the truest test of species status is the test of sympatry: whether two forms interbreed when they co-occur in nature. In this case, the two species live together side by side, and reproductive isolating barriers, such as differences in male behavior (see the original species description by Gabriele Gentile and Howard Snell), keep them genetically isolated from one another. (Gentile and colleagues did find a single individual which showed evidence of some genetic mixing, but it is evidently insufficient to breakdown the genetic isolation of the forms.) This is a really remarkable and exciting discovery, given how many scientists, park rangers, and even just tourists, have traversed these islands. (I have been to Isabela, not far, at least as the crow flies, from where the new species was discovered.)

Although I think it’s fair to say that interested scientists have been delighted by the discovery of the pink land iguana, a number have been disturbed by what Gentile and Snell did, or rather didn’t do, in naming the species: they did not collect a specimen to document the species, but relied upon blood samples and photos. Usually, when a new species of animal is described, a particular specimen is designated the holotype, and preserved and deposited in the collection of a museum that will make the specimen available for study by other scientists. The specific identity of the holotype fixes the application of the name, and study of the holotype helps resolve any questions or confusions concerning the status or identity of the species, as well as contributing to further knowledge of the species’ biology. But if there is no holotypic specimen, then other scientists are unable to check the describer’s claims, or test their conclusions, or advance the study of the species in any way. Gentile and Snell were aware that what they were doing was problematic, and addressed the question in their paper. They even designated a particular iguana as the holotype, but left it in the wild, hoping that at some later time it might be retrieved using a radio tag they put in it. They did not collect it out of concern that loss of even a single individual might drive the species extinct.

Alain Dubois of the Museum nationale d’Histoire naturelle and Andre Nemesio of the Universidade Federal de Minas Gerais, Brazil, have led the criticism of Gentile and Snell, while acknowledging that there may be times when it is not wise to collect a specimen. See papers by them here, here, and here; Thomas Donegan of Fundacion Proaves supports what Gentile and Snell did. In the bad old days of systematic zoology, species were often named without holotypes, and this led to much confusion. Lately, there have been several species named for which holotypes have not been collected, for the same reasons advanced by Gentile and Snell, and this has led to much controversy; many of the key papers are cited in the woks of Dubois, Nemesio, and Donegan, or in works cited therein.

Some people might ask, what’s wrong with a photo? Well, I think it should be evident that there are many things you can’t determine from a photo, but perhaps a mention of the most famous species named on the basis of a photograph will make some of the problems clear: that species is the Loch Ness monster, Nessiteras rhombopteryx (abstract only without subscription). To put it only a bit too simply, specimens are what separate zoology from cryptozoology, science from pseudoscience. More on this in a later post.

Darwinius: what’s at issue?

May 21, 2009 • 3:10 pm

by Greg Mayer

I’m leaving in a few days for Costa Rica, and Jerry is back, so this will be my last post on Darwinius, at least for awhile. At least three different issues have been debated in the blogosphere concerning “Ida“: 1) What are her phylogenetic relationships; 2) Was the media campaign excessive; and 3) Has the name been published?

Darwinius on toast1) What are her phylogenetic relationships? This is the most important one, because it is, as John Maynard Smith once put it, about the world, and not about names. Is Darwinius close to the common ancestor of monkeys, apes, and men, or is it a member of the group that includes lemurs and lorises? The question has been raised and discussed most forcefully by Brian Switek at Laelaps, who thinks the evidence presented for relationship to monkeys and apes is weak. To my mind (and I’m not a specialist in primates or even mammals), he’s got a strong point, and we can look forward to a publication by Brian (or some other critic) on this issue.

2) Was the media campaign excessive? The short answer is yes. I expressed some uneasiness over the media campaign here at WEIT, and many others have documented the extravagant claims and consequent media misunderstandings further. See especially what Carl Zimmer had at the Loom, Brian at Laelaps, and PZ Myers at Pharyngula. But by far the best (or at least funniest) take on this was Ed Yong’s satirical evisceration of the inflated media campaign at Not Exactly Rocket Science, from which I have been kindly permitted to reproduce the by now iconic “Darwinius on Toast” above. There are many unresolved questions concerning how to present science to the public, and differing views concerning how aggressive a media campaign should be, but this one was at least one step beyond.

3) Has the name been published? This is the most technical issue, and is about names (rather than the world), but it’s attracted the most attention. See the posts here at WEIT, the Loom (and here), the Lancelet, and Laelaps, including the ensuing commentary by, among others, Henry Gee, Martin Brazeau, and Larry Witmer. There are several issues, and I’ll treat them very briefly (since this is a blog post, and not a paper in the Bulletin of Zoological Nomenclature!).  For reference, The International Code is online here.

3a) Has the name Darwinius masillae been published (in the sense of the Code) in Plosone? No. Many people have noted that Art. 8.6 requires non-paper works to be deposited in 5 major libraries, and that a statement to this effect must be included in the paper. No such statement is in the paper. More importantly, although it has been noted in only one comment I’ve seen, Art. 9 goes on to specify that nothing distributed by the web counts as being published. The non-paper works envisioned in Art. 8 are things like CDs, not web postings. So, the various remedies proposed, such as reposting on Plosone with the requisite statement, would not work. To be published, a non-Web work must be made: paper, CD, DVD (the latter two requiring the fulfillment of the 5 major libraries rule), or something else which satisfies Arts. 8 and 9.

3ai) Can the name be made available by publishing a short paper (on paper) with a bibliographic reference to the Plosone posting? No, because availability by bibliographic reference must be by reference to a published work (Art. 13.1.2), and anything on the Web is not published (Art. 9.8).

3b) Has the name been published elsewhere? I hope not, but fear it may have been. I pointed out that the various newspaper articles may count as publication, because they meet the various criteria for publication (obtainability, simultaneity, etc.; Art. 8), and also contain 1) the name, and 2) are “accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (Art. 13.11), and even follow Recommendation 13A: “a summary of the characters that differentiate the new nominal taxon from related or similar taxa.” Many newspaper articles, in addition to a general description, included explicit differentia– incisors, grooming toes– from related taxa, thus providing a diagnosis.

3bi) Can newspapers provide a public and permanent scientific record? In my post, I considered that the newspaper articles might be discounted, because perhaps they had not been issued “for the purpose of providing a public and permanent scientific record” (Art. 8.1.1). Some commenters have taken the position that this is self-evidently the case, but it’s not crystal clear to me.  The Code has always been loath to mandate specific formats of publication, specifying rather general properties (availability, simultaneity, identity, etc.) that a variety of formats might fulfill.  Historically, a huge variety of things have counted as publications (although no newspaper examples come to mind). Some newspapers have science sections, some are “papers of record”; I think the spirit of the Code is to approach each case on its individual merits. That is why the Code urges authors and editors to avoid anything that might make the situation murky, but it does so through recommendations (see my previous post for the specific recommendations).

3bii) Doesn’t the Code try to avoid “accidental” publication? Yes it does, as several commentators have pointed out. It has added meeting and symposium abstracts to the list of formats that are not permissible (Art. 9.9) to help avoid what the Code calls “unintentional publication”; but newspapers, as such, are not mentioned. The Code also now requires that the intention to establish a new name be explicit (Art. 16.1). This article is intended to prevent new names, especially a replacement name (nomen novum) to be introduced without mention, en passant if you will. Unfortunately, the newspaper articles make it absolutely clear that a new nominal taxon has been discovered and is being given a new name, and that this is the intention of the authors (on which, see next paragraph).  The Daily Mail article even uses the word “christened”. The Code urges authors to use “sp. nov.” or some other appropriate indication (Rec. 16A), but, again, does not require it. The Code recommends that any appearance of a new name in a work prior to its intended publication be accompanied by a disclaimer, making the new name unavailable (Art. 8.2 and Rec. 8D). The Daily Mail article contains the phrase “a scientific study to be published”: this might be taken to be such a disclaimer, and while it’s not as clear as one might want, it’s perhaps the most straightforward way of discounting the Daily Mail article. Such phrases may (or may not) appear in the other newspaper articles.

3biii) If it has been published elsewhere, who is the author of the name? The Code provides that when it is clear from the contents of a publication that the name and the conditions that make it available other than publication (i.e. the description or diagnosis) are the work of a person(s) other than the author of the publication, then the author of the name is the other person (Art. 50.1.1). In this case, the newspaper articles make clear that the name and its description were provided by someone else, many mentioning Jorn Hurum and Phil Gingerich. They (or whoever is mentioned in the earliest article published) are thus the authors.  This is a good thing, because it gives credit to at least some of the people actually involved in the work. The newspaper reporter would not be the author of the name.

To summarize the question of publication, the name has not been published in Plosone, but it may have been published in a newspaper. I hope the latter is not the case, and perhaps the Commission could issue a clarifying opinion (following an appropriate application) on the status of names published in newspapers (the problem may be distinguishing newspapers from newsletters from cheaply printed bulletins, and so on).

There are some other issues that have been discussed– the merits of paper vs. the web, the nature of peer review– but these go well beyond the particulars of Darwinius, although it might provide a case study for some of these issues. But one of the take home lessons here is that the recommendations of the Code should be taken to heart, and authors and editors should ensure that works affecting nomenclature are “self-evidently published within the meaning of the Code“(Rec. 8B), and that new names should not appear in works prior to their intended publication, or, if they do, they should “contain a disclaimer (see Article 8.2), so that new names published for the first time therein do not enter zoological nomenclature unintentionally and pre-empt intended publication in another work” (Rec. 8D).

Update. While I was writing this, Carl Zimmer got a reply from the Executive Secretary of the ICZN. She confirms that posting on Plosone does not make a name nomenclaturally available. The issue of the newspaper publication was not addressed; I’m not sure if Carl asked about this. I’m leaning myself toward the idea that inclusion of the statement that the study is going to appear somewhere else could be construed as a disclaimer, thus avoiding newspaper publication of the name (I’m still not sure that all newspaper articles included such a statement).

Update 2. Carl Zimmer at the Loom has a nice account of the PR run-up to the press conference, which he titles “Science Held Hostage“. And, also from Carl, Plosone has today printed a 50 copy paper edition. If we can dismiss the newspaper versions (which, as I indicate in my first update, I think we can because they can be plausibly interpreted to have a disclaimer), then the name is now published with the intended authorship; the date of publication is 21 May 2009 (not 19 May, which is when it was posted to the web). Carl also succinctly explains why the nomenclatural rules are necessary:

To those not steeped in species, genera, suborders and suprafamilies, all of these bylaws and codes may trigger vertigo. But keeping the world’s biodiversity in order is not for the faint of heart. With 1.8 million species on the books, and tens of thousands of new ones being added every year, taxonomists need an intricate set of rules to keep it all straight. The fact that taxonomists share a set of rules, no matter how intricate, was one of the great advances in the history of biology.

Has the name Darwinius masillae been published? And if so, by who?

May 20, 2009 • 1:27 pm

by Greg Mayer

In a previous post on the hype surrounding the online posting of a paper on ‘Ida’, the Eocene primate from the Messel Lagerstatte, I noted that the

from Hurun et al. 2009. Plosone.
from Franzen et al. 2009. Plosone.

authors had made a nomenclatural faux pas in allowing the name and a description to be published before their paper appeared, thus making the authorship and date of publication of the name murky. At Laelaps, cromercrox (comment 35 here and comment 16 here), and at the Loom, Martin Brazeau and Larry Witmer (comments 27 & 29) have also noted nomenclatural problems, since online posting does not constitute publication under the International Code of Zoological Nomenclature, unless copies “have been deposited in 5 major publicly accessible libraries which are identified by name in the work itself”, (ICZN 8.6), which didn’t happen. As posted by Plosone, the paper is not published for nomenclatural purposes.

My concern was not that the name was unpublished, but that it had already been published, in one or more of the newspapers or perhaps even magazines that covered the pre-press conference hoopla. In the Code, Article 8 defines publication, Articles 10 and 11 cover general conditions of availability of a name, and Article 13 gives the particulars for names published after 1930 (the rules are stricter after 1930). The requirements may be summarized by saying that a proper new name must be published (sensu Article 8), and must “be accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (ICZN 13.1.1). I fear these requirements have been met by some of the pre-press conference articles.

The earliest one I have found is the one in the Daily Mail from May 10 (there may be earlier ones– I haven’t looked very hard). (I also don’t have a paper copy, and am assuming the web article appeared in the paper.  If it didn’t, I could illustrate the exact same points for the New York Times, for which I do have paper copies.) In the article, by Sharon Churcher, the name appears:

Christened Darwinius masillae, it belonged to an extinct group of primates which lived in rainforests.

It also includes characters that are purported to differentiate the taxon:

The study’s authors insist that the fossil can’t be a lemur because it lacks two features: the ‘toothcomb’, a set of lower front teeth used to groom fur; and ‘toilet claws’, toes on the hind feet used for scratching.

The Mail is also mass produced in identical copies obtainable for free or by purchase, publicly available, and permanently archived in many libraries. So it looks like the name has been published.  The one possible out is that you could argue that the Mail isn’t issued for the purpose of providing a scientific record, but purposes are slippery things. Does a newspaper with a science section (which is of course quite purposeful) meet the requirement, but perhaps one without doesn’t? I don’t know. That’s why it’s murky. It is to avoid murkiness that the Code makes Recommendation 8B:

Authors and publishers are strongly urged to ensure that a new scientific name or nomenclatural act is first published in a work printed on paper.

also Recommendation 8D:

Authors, editors and publishers have a responsibility to ensure that works containing new names, nomenclatural acts, or information likely to affect nomenclature are self-evidently published within the meaning of the Code. Editors and publishers should ensure that works contain the date of publication, and information about where they may be obtained. (emphasis added)

and Recommendation 8E:

Editors and publishers should avoid including new names and the information that might appear to make the names available, or new nomenclatural acts, in works that are not issued for public and permanent scientific record (such as pre-symposium abstracts, or notices of papers to be delivered at a meeting). They should ensure that such documents contain a disclaimer (see Article 8.2), so that new names published for the first time therein do not enter zoological nomenclature unintentionally and pre-empt intended publication in another work. (emphasis added)

But it looks to me like the Mail (or the Times, or whoever published it first) is the first valid publication of the name. The Code provides that the author of a name need not be the author of the work:

However, if it is clear from the contents that some person other than an author of the work is alone responsible both for the name or act and for satisfying the criteria of availability other than actual publication, then that other person is the author of the name or act. If the identity of that other person is not explicit in the work itself, then the author is deemed to be the person who publishes the work. (ICZN 50.1.1; emphasis added)

Jorn Hurum and Phil Gingerich are mentioned in the article as people who did the work, with Hurum given precedence.  So what’s the proper citation of this new taxon? It’s

Darwinius masillae Hurum and Gingerich in Churcher 2009.