Tetrapod Zoology

As you may know, Tet Zoo has been going for four years now. Despite this, there are still entire tetrapod clades – consisting of hundreds or even thousands of species – that have scarcely been mentioned here, if at all.

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Lately, I’ve been feeling ‘gecko guilt’. Yes, I can barely believe that the enormous squamate clade known as Gekkota has been all but unmentioned on these pages. I don’t have time to give the group any sort of justice (sorry, Gekkota), but here is a very brief intro to the group and how neat it is (aaaaand, as usual I wrote this sentence long before completing what you’re about to read…).

Gekkotans occur worldwide as more than 1500 species (some sources give figures of 2000 or so… if you keep an eye on the herpetology journals, you’ll know that new gekkotan species are constantly being described): they inhabit all continents except Antarctica, have done extremely well at colonising oceanic islands, and inhabit temperate regions (such as New Zealand) as well as subtropical and tropical ones. Most have well-developed limbs, but near-limblessness has also been evolved in the group. Indeed, because the near-limbless flap-footed lizards, snake lizards, pygopods or pygopodids are gekkotans, the term ‘gecko’ is not synonymous with Gekkota… unless you’re happy referring to pygopodids as geckos, and nobody really does that (… much. I have seen it done here and there) [the pygopodid Liasis burtoni (Burton's snake lizard) shown above; image courtesy of Wolfgang Wüster].

I’m going to use the spelling ‘gecko’ and ‘geckos’ here, but ‘gekko’ and the plural ‘geckoes’ are used by some.

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Gekkotans are mostly ‘mid-sized’ lizards (with total lengths of 15 cm or so), but many are dwarfs. One species – Sphaerodactylus ariasae from the Dominican Republic – is adult at 1.6 cm [an S. macrolepis specimen from Puerto Rico shown here; photo by Samuel Thomas, from wikipedia]. The largest gekkotan – recently extinct Hoplodactylus delcourti from New Zealand* – reaches or reached 60 cm. There have never been any giant gekkotans so far as we know, nor are there any amphibious or aquatic ones.

* Probably. Worthy & Holdaway (2002) expressed scepticism about a New Zealand origin for this species (even though all other Hoplodactylus species are New Zealand endemics), only because additional specimens have never been found (the only known specimen – shown below, from wikipedia – was discovered in a French museum and its exact origin is unknown). I think it’s most likely that H. delcourti was endemic to New Zealand; it’s just that we have yet to find additional specimens (Naish 2004).

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Introducing the cast

For ease of communication, I have to introduce the names of the main gekkotan groups now (their affinities and such will be covered later). As mentioned a moment ago, there are something like 1500-2000 gekkotan species but, as usual with herps, there’s nothing like a World Guide to Gekkotan Species – would anyone like to pay me to write one? If you’re in search of an introduction to the clade, good places to start are Mattison (1989), Bauer (2000) and Pianka & Vitt (2003). If you want to learn about the group on an intimate, species-level basis (good for you), you’ll have to rely on the primary literature, or on field guides. Among the best of the latter for gekkotans are Branch (1988), Cogger (2000)* and Spawls et al. (2004).

* Given its substantial weight I’m not sure it can be classed as a ‘field guide’…

As you’d expect for a group that includes 1500-2000 species, there’s a significant amount of disparity within the clade, and fossils indicate that some of the major divergences within Gekkota happened in the early Cenozoic or as long ago as the Cretaceous. If gekkotans were birds or mammals, they’d have been classified into something like 50-100 ‘families’ or more, or even into several separate ‘orders’. But, no, these are reptiles, so people have mostly been happy with a classification where all of those species, spanning an evolutionary history of more than 50 million years, are grouped into two – yes, TWO – family-level groups (namely, Gekkonidae and Pygopodidae). Huh. I’m not necessarily saying that a new classification is needed: my point is that ‘historical inertia’ has shaped our perception of diversity across the tetrapod clades (see Frost et al. (2006) for more on this subject). Anyway, in the scheme followed here, five main gekkotan groups are recognised: eublepharids, diplodactylines, pygopodids, gekkonids and sphaerodactylids. A sixth proposed clade might also exist: the phyllodactylids.

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A relatively small number (c. 25 species) of terrestrial North American, African and Asian gekkotans are grouped together in Eublepharidae. The best known eublepharid is the familiar Leopard gecko Eublepharis macularius of southern Asia [shown here: photo by Fritz Geller-Grimm, from wikipedia]. Because they lack digital pads and possess eyelids, eublepharids have typically been regarded as morphologically primitive compared to other living gekkotans.

The vast majority of gekkotan taxa are part of Gekkonidae, and this group has often been divided into two ‘subfamilies’: Gekkoninae and Sphaerodactylinae. Gekkoninae has conventionally been thought to include such geckos as Cyrtodactylus (bow-fingered geckos), Phelsuma (day geckos), Gekko (calling geckos), Phyllodactylus (American leaf-toed geckos), Ptychozoon (flying geckos), Tarentola (wall geckos) and Uroplatus (leaf-tailed geckos). Typically, five genera have been included within Sphaerodactylinae (Coleodactylus, Gonatodes, Lepidoblepharis, Pseudogonatodes and Sphaerodactylus), all of which inhabit the Caribbean and South and Central America. This group of genera is best known for including numerous tiny species. However, some studies (e.g., Gamble et al. 2007) find these taxa to be part of a more inclusive clade that also includes several Old World taxa, among which are the wonder geckos or frog-eyed geckos (Teratoscincus). The name Sphaerodactylidae has been used for this ‘expanded’ sphaerodactyl clade. Phyllodactylus and an assemblage of other taxa (Asaccus, Haemodracon, Homonota, Phyllopezus, Ptyodactylus, Tarentola and Thecadactylus) have recently been allied in a molecular phylogeny and named as the new clade Phyllodactylidae (Gamble et al. 2008). Phyllodactylids are the sister-group to Gekkonidae according to these authors. To date, only a few other authors have used the name Phyllodactylidae (e.g., Blair et al. 2009) and it will be interesting to see if other studies support the monophyly of this proposed clade.

Diplodactylines or diplodactylids are an entirely Australasian group that seem to form a clade with the snake-like pygopodids (Kluge 1987, Donnellan et al. 1999, Conrad 2008). Some diplodactylines – including knob-tailed geckos (Nephrurus), New Caledonian geckos (Rhacodactylus) and chameleon geckos (Carphodactylus) – are sometimes grouped together as the carphodactylids, carphodactylines or carphodactylins. They might warrant distinction relative to diplodactylines (and may be closer to pygopodids than diplodactylines are), might be a diplodactyline clade, or might be a grade within diplodactylines.

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A few other gekkotan groups have sometimes been recognised. Teratoscincus was considered worthy of its own ‘subfamily’, termed Teratoscincinae, by Kluge (1987) [T. keyserlingii shown here; from wikipedia]. The Cat gecko Aeluroscalabotes felinus of south-eastern Asia has also been given its own ‘subfamily’ on occasion, dubbed Aeluroscalabotinae (modern classifications generally include A. felinus in Eublepharidae) while a group of African gekkonines have sometimes been referred to as the Ptyodactylini.

We’ll look at gekkotan phylogeny later on. Much more to come. Coming next: voices, eggshells and cervical sacs.

For previous Tet Zoo articles on neat squamates see…

Refs – -

Bauer, A. M. 2000. Lizards. In Cogger, H. G., Gould, E., Forshaw, J., McKay, G. & Zweifel, R. G. (consultant eds) Encyclopedia of Animals: Mammals, Birds, Reptiles, Amphibians. Fog City Press (San Francisco), pp. 564-611.

Blair, C., Méndez de la Cruz, F. R., Ngo, A., Lindell, J., Lathrop, A. & Murphy, R. W. 2009. Molecular phylogenetics and taxonomy of leaf-toed geckos (Phyllodactylidae:
Phyllodactylus) inhabiting the peninsula of Baja California. Zootaxa 2027, 28-42.

Branch, B. 1988. Field Guide to the Snakes and Other Reptiles of Southern Africa. New Holland (London).

Cogger, H. G. 2000. Reptiles & Amphibians of Australia (Sixth Edition). New Holland Publishers (Sydney).

Conrad, J. L. 2008. Phylogeny and systematics of Squamata (Reptilia) based on morphology. Bulletin of the American Museum of Natural History 310, 1-182.

Donnellan, S. C., Hutchinson, M. N. & Saint, K. M. 1999. Molecular evidence for the phylogeny of Australian gekkonoid lizards. Biological Journal of the Linnean Society 67, 97-118.

Frost, D. R.., Grant, T., Faivovich, J., Bain, R. H., Haas, A., Haddad, C. F. B., De Sá, R. O., Channing, A., Wilkinson, M., Donnellan, S. C., Raxworthy, C. J., Campbell, J. A., Blotto, B. L., Moler, P., Drewes, R. C., Nussbaum, R. A., Lynch, J. D., Green, D. M. & Wheeler, W. C. 2006. The amphibian tree of life. Bulletin of the American Museum of Natural History 297, 1-370.

Gamble, T., Bauer, A. M., Greenbaum, E. & Jackman, T. R. 2007. Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. Journal of Biogeography 35, 88-104.

- ., Bauer, A. M., Greenbaum, E. & Jackman, T. R. 2008. Out of the blue: a novel, trans-Atlantic clade of geckos (Gekkota, Squamata). Zoologica Scripta 37, 355-366.

Kluge, A.G. 1987. Cladistic relationships in the Gekkonoidea (Squamata, Sauria). University of Michigan Museum of Zoology Miscellaneous Publications 173, 1-54.

Mattison, C. 1989. Lizards of the World. Blandford (London).

Naish, D. 2004. New Zealand’s giant gecko: a review of current knowledge of Hoplodactylus delcourti and the kawekaweau of legend. The Cryptozoology Review 4 (2), 17-21.

Pianka, E. R. & Vitt, L. J. 2003. Lizards: Windows the Evolution of Diversity. University of California Press (Berkeley).

Spawls, S., Howell, K., Drewes, R. & Ashe, J. 2004. A Field Guide to the Reptiles of East Africa. A & C Black (London).

Worthy, T. H. & Holdaway, R. N. 2002. The Lost World of the Moa. Indiana University Press (Bloomington, Indiana).

Comments

  1. #1 Dartian
    April 22, 2010

    unless you’re happy referring to pygopodids as geckos, and nobody really does that (… much. I have seen it done here and there)

    Funny, I’ve always been quite happy to think of pygopodids as nothing but aberrant geckos. (Of course, I’m an utter non-specialist regarding squamate phylogeny.)

  2. #2 Rosel
    April 22, 2010

    Yay geckos! my favourite type of lizard, I wish we had them in England, I miss scouring the desert for them.

  3. #3 David Marjanović
    April 22, 2010

    Thanks for pointing out the vile effects of the rank-based approach to biodiversity. The geckos are so neglected in the tertiary and secondary literature that even I had no idea there are 1500 to 2000 species!!!

  4. #4 winston
    April 22, 2010

    “Most have well-developed limbs, but near-limblessness has also been evolved in the group” – I was wondering: do you maybe know how many digits geckos have and how constant is the number of digits (in a given species do all individuals have the same number)? And do the limbless species initiate a developmental program (ie limb budding) during embryogenesis, as dolphins do? I don’t know much about geckos, but I’ve seen pictures with four and five digits, so I was wondering…

  5. #5 Carlos
    April 22, 2010

    Its sad no one really focuses on the imense diversity of squamate species. Burn the bird guides, I want a guide of gecko species in Eurasia!

  6. #6 Anonymous
    April 22, 2010

    “Despite this, there are still entire tetrapod clades – consisting of hundreds or even thousands of species – that have scarcely been mentioned here, if at all.”

    Good news, it doesn’t look like you’re going to run out of material anytime soon. Bad news, it looks like you have a looot of work ahead of you.

    “But, no, these are reptiles, so people have mostly been happy with a classification where all of those species, spanning an evolutionary history of more than 50 million years, are grouped into two – yes, TWO – family-level groups (namely, Gekkonidae and Pygopodidae).”

    While in many cases the idea of splitting versus lumping can be argued from either side, I think a lot of people would probably agree that geckos are really overlumped. Unless all of these species within the various genera can interbreed with one another, that is.

    “There have never been any giant gekkotans so far as we know, nor are there any amphibious or aquatic ones.”

    My guess for this is that other squamates, such as monitors and such, have the headstart on the geckos whenever such a niche opens. Maybe if you put them on an island with just geckos you’d get better results.

    “but here is a very brief intro to the group and how neat it is”

    I assume you are going to have to mention the gecko Pseudophelsuma bipes, a six-inch or so long gecko from Madagascar (despite being commonly mistaken for an Australian species), and has the odd ability to stand on its hind legs like a perentie monitor.

  7. #7 Darren Naish
    April 22, 2010

    Winston (comment 4): the majority of gekkotans have 5 fingers and 5 toes, but manual digit I has been lost several (or many) times (in various species of Phelsuma and Lygodactylus, for example). Pedal digit I is strongly reduced in many Phelsuma and Lygodactylus species as well, but I don’t know if any lack this digit entirely. So far as I know, the members of a species are consistent with regard to how many digits they have (correct this if you know otherwise!).

    Do limbless pygopodids develop limb buds during their embryology? I don’t know: just did a quick check of the literature and couldn’t find an answer. Does anyone know? Incidentally, note that I referred to pygopodids as ‘near-limbless’. This is because they’re not completely limbless – they still have flap-like hindlimb remnants.

  8. #8 Chelydra
    April 22, 2010

    @Anonymous:

    The complaint is not so much about lumping versus splitting, but that a bias has resulted because herpetologists have mostly lumped while mammalogists and ornithologists have split when it comes to recognizing clades higher than species level. Based on current classifications (via Wikipedia), there are about three times as many reptile species per family, and four times as many amphibian species per family, as there are mammal or bird species per family. To the casual observer this would seem to imply that herpetofauna aren’t as diverse as birds or mammals, even though in reality the differences may be entirely due to historical lumping biases or merely opinions on what level of the taxonomic “hierarchy” a clade belongs. Case in point: according to current classification, it is implied that a chicken (order Galliformes) is as different from a duck (order Anseriformes) as a turtle (order Testudines) is from a snake (order Squamata), which is ridiculous.

  9. #9 Jura
    April 22, 2010

    It’s nice to know that I’m not the only one who notices the way that reptiles tend to get overlooked in the literature (e.g. another reason for a lack of field guides on geckos is because we don’t know the natural history of the majority of them).

    @David Marjanovic – the super lumping has nothing to do with rank based systems, and everything to do with a pro-fuzzball bias.

  10. #10 Zach Miller
    April 22, 2010

    Whoo! Thanks for covering leopards and frog-eyes, Darren! I’ll be interested to see where frog-eyed geckos fall on the gecko family tree. They lack eyelids, but they have large, overlapping scales. They can’t crawl up walls, but they’re very good diggers thanks to their laterally-expanded toes that are equipped with “hairs” for grippage, I imagine.

  11. #11 John Harshman
    April 22, 2010

    Chelydra:

    Whose current classification? Under the most prevalent recent classification, under which turtles aren’t diapsids, snakes and birds fall into a clade that excludes turtles. Then again, under another suggested recent classification, turtles and birds are both archosaurs, while snakes are lepidosaurs. I hope you aren’t talking about that silly paraphyletic group “Reptilia”.

  12. #12 retrieverman
    April 22, 2010

    You left out this gecko:

    http://www.youtube.com/watch?v=acCfnwTpdxU

    I hope he appears in the other posts.

  13. #13 Keir
    April 22, 2010

    “as usual with herps, there’s nothing like a World Guide to Gekkotan Species – would anyone like to pay me to write one?”

    I’d pay to see a guide to the amphisbaenia! Sure, the species only number about a tenth of the gekko species, but that should only make the task easier. I love to watch them move, it is different from a snake, and really hypnotic.
    For the curious:
    http://www.youtube.com/watch?v=LoyrON_kGKw
    http://www.youtube.com/watch?v=mqi34DVLMWI

  14. #14 Zach Miller
    April 22, 2010

    “Reptilia” is still a perfectly valid term, with the understanding that it includes the common ancestor and all decendants of turtles, squamates, and archosaurs. It doesn’t necessarily have to replace the term “Sauropsida,” which can be more inclusive. It can simply refer to the crown group.

  15. #15 John Scanlon, FCD
    April 22, 2010

    Do limbless pygopodids develop limb buds during their embryology?

    Don’t know if embryos have been looked at, but Greer (1989: 97-98) reconstructs the LCA of Pygopodids with (slightly paraphrased): all external trace of front limbs lost, but small remnant of humerus present internally; rear limbs reduced to small flap-like appendage with femur, tibia and fibula, some tarsals, four metatarsals, and a single phalanx [he writes 'phalange'] in each of the two middle digits; pectoral girdle containing all of the basic elements in a reduced state, and with only two ribs attached to the sternum, and no mesosternum; pelvic girdle with all basic elements but reduced and widely separated across the midline; sacral diapophyses separated from each other distally and with loose ligamentous connection to ilium; attenuate body at least nine times head length, with at least 44 trunk vertebrae.

    There have never been any giant gekkotans so far as we know, nor are there any amphibious or aquatic ones.

    I dunno, H. delcourti and some of the Rhacodactylus are what I’d call giant geckos, but I see what you mean. They’re definitely in the Varanus size range (probably not coincidentally, on islands never reached by varanids, cf. Anonymous #6), but pretty far from komodoensis or even varius. New Cal also produced some big scary skinks (big skinks elsewhere are mainly herbivorous, not predators on other vertebrates).

    fossils indicate that some of the major divergences within Gekkota happened in the early Cenozoic or as long ago as the Cretaceous

    But there’s been a rash of molecular clock papers on squamates (etc.) concluding much older dates than actual fossils would support; some include dodgily-identified fossils, but all seem to use calibrations based on geological age of islands and mountain ranges (thus assuming strict vicariance) but it turns out the phylogenies always imply various long-distance dispersals…

    Greer, A.E. 1989. The Biology and Evolution of Australian Lizards. Surrey Beatty & Sons, Chipping Norton NSW.

  16. #16 Anonymous
    April 22, 2010

    “You left out this gecko:

    http://www.youtube.com/watch?v=acCfnwTpdxU

    I hope he appears in the other posts.”

    Joke’s already been made, man.

  17. #17 Sebastian Marquez
    April 22, 2010

    Predaceous giant skinks of New Caledonia? Wow, I never knew.

    Awesome article by the way. Geckos were the first squamates I ever interacted with; I remember catching them with makeshift palm-leaf lassos in the Philippines as a kid.

  18. #18 Hai~Ren
    April 22, 2010

    John:

    They’re definitely in the Varanus size range (probably not coincidentally, on islands never reached by varanids)

    Wasn’t there a monitor lizard on New Caledonia? It’s mentioned in this post.

  19. #19 retrieverman
    April 23, 2010

    What about this one?

    http://www.youtube.com/watch?v=7upG01-XWbY

    He’s not there either.

    And you just said “Gekko” was a variant.

  20. #20 John Scanlon, FCD
    April 23, 2010

    Thanks Hai-Ren, I’d missed that New Cal goanna also being mentioned by Molnar (2004) who cites Balouet (1991)… which it turns out I also have here (checking…)

    Crap, I wish I’d remembered I had that paper when I started finding Mekosuchus bones! – plate 3 has more pieces illustrated than the two original papers on M. inexpectatus. Also the Varanus cf. indicus material shown (pl. 2) is beautifully preserved, but there’s no indication of scale in the figure or text (which is not very clearly written). Particularly long teeth seem to be its most distinctive feature, which probably means dietary specialization (but on what?).

    So yeah, there used to be a varanid species in New Cal but not an endemic radiation like the skinks and geckos there, so the varanid probably got there much later.

    Balouet, J.C. 1991. The fossil vertebrate record of New Caledonia. Pages 1383-1409 in P. Vickers-Rich, J.M. Monaghan, R.F. Baird and T.H. Rich (eds), Vertebrate Palaeontology of Australasia. Pioneer Design Studio, Melbourne.

    Molnar, R.E. 2004. The long and honorable history of monitors and their kin. Pages 10-67 in E.R. Pianka, D.R. King and R.A. King (eds), Varanoid Lizards of the World. Indiana University Press, Bloomington & Indianapolis.

  21. #21 Darren Naish
    April 23, 2010

    Many thanks to all for comments.

    On divergences within Gekkota, John (comment 15) urges caution, given that molecular phylogenies suggest older divergences than those supported by fossils. Gamble et al. (2007), for example, show all gekkotan clades originating in the Cretaceous. Yeah, I’m aware of this so tried to be cautious: I specifically checked that there were old fossils that seemed to evidence ancient divergence. And Cretaceogekko burmae from Mynmar was suggested by Arnold & Poinar (2008) to be a gekkonid. Furthermore, the immaculately preserved Yantarrogekko is Lower Eocene and also seems to be a gekkonid (Bauer et al. 2005). It also, therefore, indicates that most divergences had occurred by this time, if not earlier.

    The big predatory, New Caledonian skink that John refers to is Phoboscinus bocourti, sometimes called the Terror skink. It’s about 50 cm long and has been described on occasion as “the T. rex of skinks” – it has big, nasty teeth and is an arch predator. What’s particularly remarkable is that, after being discovered prior to 1876, it disappeared and was thought extinct (this is why it’s in Flannery & Schouten’s A Gap in Nature). However, a live one turned up in 2003! I have plans to cover skinks at some stage – there’s a lot to say about them.

    Refs – -

    Arnold, E. N. & Poinar, G. 2008. A 100 million year old gecko with sophisticated adhesive toe pads, preserved in amber from Myanmar. Zootaxa 1847, 62-68.

    Bauer, A. M., Böhme, W. & Weitschat, W. 2005. An Early Eocene gecko from Baltic amber and its implications for the evolution of gecko adhesion. Journal of Zoology 265, 327-332.

    Gamble, T., Bauer, A. M., Greenbaum, E. & Jackman, T. R. 2007. Evidence for Gondwanan vicariance in an ancient clade of gecko lizards. Journal of Biogeography 35, 88-104.

  22. #22 David Marjanović
    April 23, 2010

    @David Marjanovic – the super lumping has nothing to do with rank based systems, and everything to do with a pro-fuzzball bias.

    The ranks are what makes the bias possible in the first place. If there weren’t any families to count, nobody could get misled by geckos having fewer families than artiodactyls!

    Indeed, the ranks require some bias of some sort, because they cannot help implying that taxa at the same rank are somehow equivalent, which is never the case.

    I hope you aren’t talking about that silly paraphyletic group “Reptilia”.

    Wikipedia is.

    Worse yet, it sometimes calls it “Sauropsida”, which is even worse — Sauropsida has been used for a clade ever since Huxley coined it.

    It doesn’t necessarily have to replace the term “Sauropsida,” which can be more inclusive. It can simply refer to the crown group.

    Unless turtles are diapsids, Sauropsida and its crown-group have the same known contents so far.

    four metatarsals, and a single phalanx in each of the two middle digits

    So, phalangeal formula x-0-1-1-0?

    However, a live one turned up in 2003!

    WTF! How did I manage to overlook that!!!

  23. #23 Darren Naish
    April 23, 2010

    On the subject of big lizards being rediscovered, did you hear about the just-announced rediscovery of the giant species Hoplodactylus duvaucelii on the New Zealand mainland? A specimen was killed in a mousetrap.

  24. #24 Rosel
    April 23, 2010

    “I have plans to cover skinks at some stage – there’s a lot to say about them.”

    Wow, it’s like birthday and christmas all at once!

  25. #25 Anonymous
    April 23, 2010

    “Predaceous giant skinks of New Caledonia? Wow, I never knew.”

    Darren, maybe instead of writing an article just on the sylviornithes, you should do a series of articles on the strange lost world-esque fauna of New Calidonia. I mean they have the kagu, terror skinks, monitors, mekosuchines, Sylviornis, and meiolanid turtles.

  26. #26 Jura
    April 23, 2010

    David Marjanovic wrote:

    The ranks are what makes the bias possible in the first place. If there weren’t any families to count, nobody could get misled by geckos having fewer families than artiodactyls!

    The bias was present long before the taxonomic system. All removing the rank system would do would get rid of the concept of a “family.” So instead of Gekkota having fewer families than Artiodactyla, we would have biologists talking about how much more speciose Artiodactyla is over Gekkota; or how many more clades are present in Clade X, over clade Y etc.

    Switching to a cladistic based taxonomic system does nothing to solve the problem of over splitting/lumping.

    Indeed, the ranks require some bias of some sort, because they cannot help implying that taxa at the same rank are somehow equivalent, which is never the case.

    Taxa of the same rank should be equivalent. Indeed the only real problem with the rank based system is that it lacks a set of standards for what constitutes each rank.

  27. #27 David Marjanović
    April 24, 2010

    the just-announced rediscovery of the giant species Hoplodactylus duvaucelii

    Oho!

    The bias was present long before the taxonomic system.

    Before Linnaeus?

    All removing the rank system would do would get rid of the concept of a “family.” So instead of Gekkota having fewer families than Artiodactyla, we would have biologists talking about how much more speciose Artiodactyla is over Gekkota;

    But then they’d have to explain why they chose just those two clades to compare.

    or how many more clades are present in Clade X, over clade Y etc.

    You mean how many cladogeneses can be reconstructed for each?

    a cladistic based taxonomic system

    There is no such thing. Sorry for sounding like a broken record, but it can’t be said often enough.

    Cladistics is the method for generating and testing phylogenetic hypotheses. Neither taxonomy or nomenclature follow from that.

    Phylogenetic nomenclature is a set of rules on how to write labels and how to tie them to a tree — to a phylogenetic hypothesis. How that hypothesis was arrived at (cladistics, stratophenetics, dreaming) doesn’t matter.

    Indeed the only real problem with the rank based system is that it lacks a set of standards for what constitutes each rank.

    That’s one problem, and it’s compounded by the further problem that no proposals for such standards have ever turned out to be workable.

    Another is that there are never enough ranks, which forces people to not name taxa they actually want to talk about. In 1995, shortly before I abandoned ranks, I made a classification of dinosaurs that had Dinosauria as a class and Neornithes as a superfamily* — at the cost of not naming Tetanurae, for instance!

    * I didn’t know yet that the ICZN doesn’t allow that; I’d have needed to call it either an infraorder or… Passeroidea or Vulturoidea or something.

  28. #28 David Marjanović
    April 24, 2010

    forces people to not name taxa they actually want to talk about

    Example: Suppose Vertebrata is a subphylum, and Amphibia and Mammalia are classes. The names Gnathostomata, Tetrapoda, and Amniota are widely used in the literature; suppose you want to have all three in your classification.

    The only halfway conventionally used rank between subphylum and class is the superclass. So, you have to arbitrarily pick one of the three names, assign the rank of superclass to it, and pretend the other two names don’t even exist.

    The rank of infraphylum is occasionally used. So you’re allowed to use two of the three names and send only one down the memory hole.

    Many proposals for more ranks, especially for more prefixes, exist, but none of them has been widely adopted, because they all get very confusing very quickly.

    Coming up with more examples is very easy (I’ve thought of two already); I’m sure you can do the same.

  29. #29 Andreas Johansson
    April 24, 2010

    Another is that there are never enough ranks, which forces people to not name taxa they actually want to talk about. In 1995, shortly before I abandoned ranks, I made a classification of dinosaurs that had Dinosauria as a class and Neornithes as a superfamily* — at the cost of not naming Tetanurae, for instance!

    Hm. If Neornithes are a supefamily, what does, say, Corvidae end up as? Subgenus?

    Keeping Aves as a class is probably more fun. That’d make Saurischia a superclass at minimum, Dinosauria an infraphylum, and Chordata something like a supderduperdomain.

    Add a requirement that sister groups have the same rank, and Xenoturbella gets a hyperconfederation all for itself.

  30. #30 LeeB
    April 24, 2010

    It’s good to see H. duvaucelii back on the mainland again; it was thought it only survived on offshore islands due to predation by introduced mammals.
    However although it is a big gecko at 30cm long calling it a giant might be a bit extreme when H. delcourti was 60cm long, and therefore presumably eight times the mass.

    It makes you wonder what H. delcourti fed on; perhaps not just giant weta and other large insects but flightless passerines as well.

  31. #31 David Marjanović
    April 25, 2010

    Hm. If Neornithes are a supefamily, what does, say, Corvidae end up as? Subgenus?

    I stopped at Neornithes, knowing full well the ornithologists would just laugh if I ever published that.

    hyperconfederation

    ROTFL! Day saved! :-D

  32. #32 Jura
    April 25, 2010

    David Marjanovic wrote:

    There is no such thing. Sorry for sounding like a broken record, but it can’t be said often enough.

    Cladistics is the method for generating and testing phylogenetic hypotheses. Neither taxonomy or nomenclature follow from that.

    Phylogenetic nomenclature is a set of rules on how to write labels and how to tie them to a tree — to a phylogenetic hypothesis. How that hypothesis was arrived at (cladistics, stratophenetics, dreaming) doesn’t matter.

    As we have discussed at length on the DML, “phylogenetic nomenclature” is nothing without cladistics. There are no examples of an PN system that doesn’t rely on cladistics to form its names. Saying cladistic based taxoonomy, or cladistic taxonomy is saying the same thing. Much like “non-avian dinosaurs;” insisting on calling this “phylogenetic taxonomy” is just creating a new name for the same definition. I don’t see the point in it.

  33. #33 Jaime A. Headden
    April 25, 2010

    David Marjanovic wrote (at comment #22):

    The ranks are what makes the bias possible in the first place. If there weren’t any families to count, nobody could get misled by geckos having fewer families than artiodactyls!

    Indeed, the ranks require some bias of some sort, because they cannot help implying that taxa at the same rank are somehow equivalent, which is never the case.

    This is not necessarily the case, especially when it comes to non-avian, non-mammalian taxa. There are, actually, quite a few additional variables that have resulted in authors simply not recognizing splitting taxa (which is NOT the same as “lumping”) when they coin them.

    1. Mammalian taxonomy is primarily informed by dental variation, features which are less expressive in classic reptiles and in birds (especially as the latter lack them), and mammalian tooth characters makes up almost 50% of virtually all morphological mammalian analyses, and in some cases more than that.

    2. Unlike classic reptiles, color variation in mammals and birds stem from more complex color receptors in the retina and a more complex brain, which permits more extremes in color than reptiles exhibit; as such, one may forgive mammologists and ornithologists for using color variation of pelage or plumage as a primary means of identification for most “species” that they recognize; it is, in fact, one of the ONLY criteria under which primary species identification has occured for over a hundred years. The recent advent in genetic sampling and identification is only a decade old.

    3. Only after points 1 and 2 are sampled have systematists taken to assessing the skeletal systems of reptiles, mammals and birds. Here, unlike the argument about ranks, is where the sampling has utterly failed herpetologists, as they have favored a generalized or biogeographic model and proportionate data to actual morphological variation of specific elements.

    The closest thing that mammologists, ornithologists and herpetologists have gotten to one another when it comes to morphology has been muscular and genital systems. Now, that’s bias.

    You must understand that some of the SAME systematists who have dealt with one of these groups has also dealt with the others, including Steel and Romer, and that for the most part their works have been followed. This includes the form of convention (avian and mammalian “orders,” while so few classic reptilian “orders,” have been named) and the models in which systematists feel comfortable operating in. Simply introducing the level of ranking that exists in Aves sensu stricto into Serpentes or Lacertilia alone would revise the perceived established arrangements that many herpetologists take for granted (just as mammalogists take their organization system for granted).

  34. #34 Dartian
    April 26, 2010

    Chelydra:

    merely opinions on what level of the taxonomic “hierarchy” a clade belongs

    Mis-use of scare quotes. The hierarchy is real. Any phylogeny, up to and including the whole Tree of Life, consists of clades that are hierarchially arranged. What, if anything, we human beings decide to call these clades is another matter altogether.

    Jura:

    The bias was present long before the taxonomic system.

    I’m not entirely sure about what specific bias we were discussing here, so apologies in advance if I’m commenting on something that nobody was really suggesting, but: Any attempt to even indirectly blame the use of rank-based nomenclature for the fact that there are fewer field guides of geckos/lizards/reptiles than there are of birds is a huge stretch to put it mildly. The vast majority of the general population* just is, and likely always will be, more interested in birds than in reptiles, and that’s not Linnaeus’ fault in the slightest.

    * And lest we forget, the Tet Zoo commentariat is not a representative sample thereof.

    David:

    no proposals for such standards have ever turned out to be workable

    In fairness, I’d say that Avise & Johns’ proposal to temporally standardise traditional taxonomies came pretty close, at least in principle. For those who haven’t heard of it: John Avise and Glenn Johns (1999) suggested that one should use lineage divergence dates for deciding what clade should have what rank (e.g., deciding that lineages that have diverged, say, five million years ago, or, say, in the Pliocene, should have the rank of ‘genus’), and then apply this consistently across organismal phylogeny (e.g., thereby making all Recent ‘genera’ comparable in age).

    Granted, applying this system for wholly extinct major fossil taxa would be a bit more tricky, although I don’t see why the same basic principle could not work for extinct taxa too. As far as I’m aware, the real drawback with Avise & Johns’ proposal is not a theoretical but a practical one: it is probably completely impossible to ever reach any sort of consensus among researchers regarding exactly which divergence dates to use. (For example, deciding upon a Pliocene age for genera might satisfy a mammalogist, but not an entomologist.) I say this with a tinge of disappointment; since I first learned of it, I’ve had a soft spot for the temporally standardised classification scheme, which I consider the closest thing to having an objective criterion for rank delimitation that we’re likely to get.

    In 1995, shortly before I abandoned ranks, I made a classification of dinosaurs

    You did what when? Weren’t you still in third grade or something in 1995?

    Reference:

    Avise, J.C. & Johns, G.C. 1999. Proposal for a standardized temporal scheme of biological classification for extant species. Proceedings of the National Academy of Sciences 96, 7358-7363.

  35. #35 David Marjanović
    April 26, 2010

    There are no examples of an PN system that doesn’t rely on cladistics

    Gregory S. Paul (2002): Dinosaurs of the Air, Johns Hopkins.

    Admittedly, that’s just about the only one, because almost everyone who even knows about PN is a cladist; but it still demonstrates that PN without cladistics is entirely feasible.

    to form its names.

    To form its names???

    color variation in mammals and birds stem from more complex color receptors in the retina and a more complex brain, which permits more extremes in color than reptiles exhibit

    Uh… what?

    No, except for crocodiles, diapsids generally retain the tetrachromatic vision that is normal for vertebrates (four different color receptors in the retina). Most mammals are dichromatic. I don’t see what the unmeasured “complexity” of the brain could have to do with any of this.

    And in general I don’t understand the point of your entire comment — I don’t see where it answers mine…

    Any attempt to even indirectly blame the use of rank-based nomenclature for the fact that there are fewer field guides of geckos/lizards/reptiles than there are of birds

    I wasn’t trying to do that.

    Weren’t you still in third grade or something in 1995?

    Of course I was (7th and 8th year of school altogether; born 1982). As I said, I didn’t publish.

  36. #36 David Marjanović
    April 26, 2010

    John Avise and Glenn Johns (1999) suggested that one should use lineage divergence dates for deciding what clade should have what rank

    That’s the system Hennig advocated in, IIRC, 1966; by 1981 he had abandoned it (and with it ranks in general) for the reasons you mention — very difficult to apply, and would drastically upset most or all existing classifications.

  37. #37 Jaime A. Headden
    April 26, 2010

    Dartian,

    While applicable in one sense, “hierarchy” implies a succession of superior from inferior levels, with a climb towards perfection (as implied in the original definition/use of “evolution”) by implying there is an ultimate limit in position. An infinitely nested series of organismal branching has no perfected limit, and in this case, “hierarchy” is inapplicable. This should be especially interesting when bacterial “species” can breed into other “species,” producing lineages that appear more like webs, and thus loop back on themselves instead of simply branching.

  38. #38 Dartian
    April 26, 2010

    Jaime:

    “hierarchy” implies a succession of superior from inferior levels, with a climb towards perfection (as implied in the original definition/use of “evolution”) by implying there is an ultimate limit in position

    If you tell a non-biologist that Squamata is a more inclusive taxon than Gekkonidae, which in turn is a more inclusive taxon than the clade Phelsuma, you’ll next be asked what that means in plain language. How would you go about explaining that statement, without hinting at there being some kind of hierarchial structure behind it?

    Look, I do see what you were getting at (which is why I agree that one should try to avoid using strongly value-laden words such as ‘superior’ and ‘inferior’ in these contexts). But I also think that we can’t go around worrying excessively that someone somewhere will misunderstand modern taxonomic concepts and terminology for support of some 18th century Scala Naturae bollocks.

  39. #39 Jaime A. Headden
    April 26, 2010

    It isn’t plain language, though. Almost anything as abstract as the concept of “hierarchy” (successive levels of authority, in the definitional sense) and “phylogeny” (patterning the tree of life [a phrase that is also abstract] as descent through modification) require some form of elaboration or further abstraction to break the concept down. It would be impossible to describe the concept of “science” to a nonscientist without such a breakdown, but the term is thrown around as though it were obvious. “Phylogeny” might be more obvious to most of us, but this is because it is more familiar to use than it is to which this termk is either less relevant or, as in some cases with humans, the ability to abstract is more difficult.

    How do I relate the concept of nesting clades and hierarchies? Through diagrams, illustrations, and the very few wonderful books out there on the subject, written by people who both know the subject and are able communicators between differing levels of comprehension. Teachers are in a position to do this, and in fact must teach in this manner in virtually all respects, but it fails when they do not know how to describe a half-familiar subject like “phylogeny.”

    So, look up the term hierarchy, and you get a few odd definitions:

    “1. Any system of persons or things ranked one above another.”

    This one clearly applies to the Linnaean system, but it does not apply to the unranked systems that have been developed. This is even used in linguistic hierarchy, in precisely that sense.

    To describe the nested scenario, I prefer using fossils, however: I describe bubbles containing bubbles, with the sizes of the bubbles relating to the number of containing species; if a containing bubble is the same size as one contained, I pop it and move on. Thus, each bubble has to have a different value in taxonomic inclusion, and the size of a bubble or its relation to another bubble is irrelevant.

    This is also done as an actual bush or branching diagram, and I simply say “name all the branches, buds/leaves, and the forks that they make: this is phylogenetic nomenclature.”

    Ranks are described using the classic model of a Ladder. You can probably see where a Bush and a Ladder are incomparable, so I find it difficult to see where a phrase describing the latter and being appropriated to describe the former is useful.