Comments

1. #1 Stephen Zozaya

   April 8, 2008

   Hey, great post…. but there are a few mistakes.

   V. rudicollis has never been recorded in the Philippines. There is a melanistic monitor that was recently described there, Varanus mabitang, which was described in 2001 by Gaulke and Curio. It, along with V. olivaceus, are the only two frugivorous varanid lizards.

   Also, according to Varanoid Lizards of the World (Pianka & King 2004) it is generally agreed that rudies do belong to the subgenus Empagusia, along with V. dumerilii (their closest exant relative,) V. bengalensis and V. flavescens. If you look at some photos of V. dumerilii you will notice the striking resemblance between adults of the two species. However, there is no mistaking that rudicollis snout.
   Varanus salvator has recently been split up into a few species, all of which belong to the subgenus Soterosaurus. Rudicollis seems to be much more closely related to bengalensis and dumerilii than to salvator or any of the other species belonging to Soterosaurus.

2. #2 Darren Naish

   April 8, 2008

   Hi Stephen, many thanks for comments, although I’m not so sure I see ‘a few mistakes’. I haven’t seen Pianka & King (2004) but… V. rudicollis was reported from Luzon (two records) in the Philippines by Kirschner et al. (1996): I know this is poorly known which is why I provided the reference. In turn Kirschner et al. cited Auffenberg (1988) for this (that’s his book on Gray’s monitor). V. mabitang is from Panay Island and I can’t see any indication that it explains the Luzon records of V. rudicollis.

   I’m glad you’ve mentioned the similarity between V. rudicollis and V. dumerilii, as the resemblance between the scalation on the neck is obvious. I wasn’t aware that they might be sister-taxa however. In the most recent phylogeny I have to hand (Pianka 1995: reproduced and employed more recently by Gould & MacFadden 2004), V. dumerilii and V. rudicollis are both in what might be called Empagusia but V. dumerilii is in a flavescens-bengalensis clade while V. rudicollis is in a clade with salvator (sensu lato). So.. Pianka & King (2004) provide a different take on the relationships of these species? I must get hold of that volume.

   Finally, yes all members of the salvator complex can be united in Soterosaurus Ziegler & Böhme, 1997, but I didn’t have cause to mention it.

   Ref – -

   Gould, G. C. & MacFadden, B. J. 2004. Gigantism, dwarfism, and Cope’s rule: “nothing in evolution makes sense without a phylogeny”. Bulletin of the American Museum of Natural History 285, 219-237.

3. #3 Stephen Zozaya

   April 8, 2008

   I’m not certain about every detail of the other paper, but since then no other reports of rudicollis from the Philippines has been made. According to Bennett, the original report is now considered very questionable. I speak to Daniel fairly often, although not for a month or two now, and he seemed convinced that the presence of rudicollis on Luzon is highly unlikely, although I am not completely certain. I’ll have to ask him the next time I speak with him.
   I looked over the information and it does currently group rudicollis in with the dumerilii-bengalensis-flavescens clade. I was, however, wrong about dumerilii and rudicollis being sister taxa. It seems I was recalling an older paper and forget about the more recent genetic work that has been done. The salvator complex is still believed to be more closely related to rudicollis than to any other taxa, however, rudicollis remains in empagusia for the moment. It is very likely that all of this information will change relatively soon and many of the SE Asia-Indo monitors will be reclassified in some way or another. There has been a lot of recent work done on some of the other monitor clades recently, however, not much on ‘ol empagusia.

   Pianka & King is a very good book on anything varanoid. It is however, missing quite a number of species accounts due to the fact that new monitors are being described like mad these days.

4. #4 Darren Naish

   April 8, 2008

   Cool, thanks for that info. And, yes, I recall as a kid that there were ‘about 30′ varanid species. How things have changed!

5. #5 David Marjanovi?

   April 8, 2008

   How many are there now, then?

6. #6 Darren Naish

   April 8, 2008

   Somewhere round about 70 I think. A 2002 checklist recognised 57, but since then several new species have been named (e.g. V. boehmei Jacobs, 2003, V. zugorum Böhme & Ziegler, 2005 and V. rainerguentheri Ziegler et al., 2007), and others have been split up into several (Böhme & Koch, for example, recently elevated the supposed V. salvator subspecies V. cumingi, V. nuchalis and V. togianus to species status).

7. #7 Zach Miller

   April 8, 2008

   Why are all seventy species stuffed into a single genus? Are there no real skeletal differences between them all? If we dug them out of the ground, would they be given separate generic distinctions?

8. #8 David Marjanovi?

   April 8, 2008

   If we dug them out of the ground, would they be given separate generic distinctions?

   Probably.

   You see, the problem is the definition of “real skeletal differences”: there is none. You can split and lump as you damn well please. The Preamble of the ICZN guarantees your “freedom of taxonomic thought or actions”.

   Personally, I think Varanus should be broken apart into several dozen genera, but I don’t and cannot have a scientific reason for that; it would just make the varanids more manageable, as in, making their phylogeny more visible in taxonomy.

   At least the PhyloCode won’t have this kind of problem…

9. #9 Stephen Zozaya

   April 8, 2008

   I think there around 64-67 Varanid species currently described. There are currently a few new species being described at the moment.

   It doesn’t look like Varanus will be split up any time soon.

10. #10 John Scanlon, FCD

    April 8, 2008

    Varanus species don’t seem to vary much in the skeleton, though there are a few apomorphies at the species-group sort of level. This means that describing fossil material is a bit of a pain, and if the genus were to be split, it would be nearly impossible to assign fossils to a genus. (I know, phylogenetically there’s nothing magical about a ‘genus’, but at least nobody doubts the monophyly of Varanus sensu lato, while the subgenera are probably not diagnosable, especially on incomplete fossil material).
    Does anybody know if Mertens (1942) is available as a pdf? That’s Abhandlungen der Senckenbergischen Naturforschenden Gesellschaft, vols 462, 465 & 466. The publisher still has copies of vol 466 for EUR 36.00, but I’d really like to have the other parts.

11. #11 Nathan Myers

    April 8, 2008

    How do the beetlemen *cough* entomologists deal with their overstuffed genera? Might their methods be adapted to students of the less manic (but still effulgent) orders?

12. #12 Ruth Sard

    April 9, 2008

    Not ‘lizard’ related, but in case you hadn’t noticed it yet, they’ve discovered a lungless frog. Cute little thing, if you like brown with big black eyes. There’s a small report on it in Zooillogix.

    Apart from being amphibious and therefore possibly of interest, if made me wonder… Zach Miller asked above ‘Are there no real skeletal differences between them all? If we dug them out of the ground, would they be given separate generic distinctions?’.

    Makes me wonder what kind of evidence would there be for lunglessness (or any other weird and wonderful adaptions, such as mouth brooding, or food reguritation if a lizard ever developed parental care of hatchlings) that would be missed (in lizards or anything else) if ALL that is found is skeletal or fossil evidence?

    Maybe some of the dino types fed their young the equivilent of ‘pigeon milk’.

    Possibilities, possibilities…

13. #13 Darren Naish

    April 9, 2008

    Ah yes, the good ol’ ‘nourishing vomit’ hypothesis again [reference]

14. #14 David Marjanovi?

    April 9, 2008

    How do the beetlemen *cough* entomologists deal with their overstuffed genera?

    Do they actually deal with them, apart from recognizing subgenera and species groups?

15. #15 Andreas Johansson

    April 9, 2008

    I don’t know about beetle genera, but there’s talk of splitting Drosophila, which has some 1500 species, plus another 500 or so in lesser genera nested inside Drosophila. The catch is that everyone’s favorite lab animal is not in the nominal subgenus …

    There’s an post from January at Catalogue of Organisms about this.

16. #16 David Marjanovi?

    April 9, 2008

    The catch is that everyone’s favorite lab animal is not in the nominal subgenus …

    All hail Brachydanio rerio and Takifugu rubripes.

    (Though the former seems to be an unclear case.)

    Your link doesn’t work.

17. #17 Andreas Johansson

    April 9, 2008

    Maybe it’ll work if I just paste the link here:

    http://catalogue-of-organisms.blogspot.com/2008/01/drosophila-forever.html

18. #18 TonyB

    April 9, 2008

    “All hail Brachydanio rerio and Takifugu rubripes.
    (though the former seems to be an unclear case.)”

    In a former life I was a fish-nerd, so I try to keep up on a lot of the shuffling of Genus names. Dr.Fang_Fang Kullander has reassigned Brachydanio to Danio in 2003.

    http://en.scientificcommons.org/20228315

    One of my favorite groups of fish, with new species being described seemingly every year.

19. #19 David Marjanovi?

    April 10, 2008

    Thanks for the two links, both work. So Takifugu rubripes, Danio rerio, and Sophophora melanogaster it is, then, unless the ICZN makes the latter the type species of Drosophila — the petition has been submitted.

    Does anyone have any idea of Caenorhabditis phylogeny…?

20. #20 Andreas Johansson

    April 10, 2008

    Strangely, it appears to be impossible to find out online what is the type species of Caenorhabditis. However, the paper linked to below has a list of species, the earliest named of which is C. genitalis, which apparently hasn’t been seen since 1880 ….

    http://www.wormbook.org/chapters/www_ecolCaenorhabditis/ecolCaenorhabditis.html

21. #21 Jerzy

    April 10, 2008

    I hope that Drosophila becomes Sopohophora, then molecular biologists oppose and kill all “no paraphyly of clades” nonsense.

    Just split taxonomy from nomenclature. Taxonomists should
    be prevented from creating chaos from nature conservation to genetics by renaming well known and important animals.

    I’m looking forward to see vertabrates split into 100 classes to properly attribute position of birds within theropods.

22. #22 David Marjanovi?

    April 10, 2008

    which apparently hasn’t been seen since 1880 ….

    That makes a good case for a petition to make C. elegans the type species.

    I’m looking forward to see vertabrates split into 100 classes to properly attribute position of birds within theropods.

    What you are saying is that nomenclature and Linnaean ranks should be divorced. I agree.

    BTW, clades are not paraphyletic by definition. “Clade” is a synonym of “monophylum” and is defined as “an ancestor and all its descendants.

23. #23 David Marjanovi?

    April 10, 2008

    Oops, insert a quotation mark in front of the last full stop.

24. #24 Jerzy

    April 11, 2008

    Thanks for correction.

    Well, perhaps best would be to redefine taxonomic units as “ancestor and some or all its descendants sharing common morphology”.

    This would prevent taxo-madness when distinctive group is found to be nested within uniform clade. No Sophophora melanogaster, no 100 classes of vertebrates to accomodate birds, no Cetartiodactyla and Whippomorpha.

    Note that clades-based approach inherently cannot produce stable and practicaly useful taxonomy. It is somewhat unscientific. No matter how well researched is a group of organisms and its evolution, its cladistic taxonomy is unknown. Because there is always a possibility that some unknown (possibly extinct) ofshoot underwent very rapid evolution, and taxonomic unit must be broken.

    Perhaps it is worth remembering that biologists de facto found clades useleless and don’t use them. We talk about great apes, elephants, artiodactyls, antelopes, raptors, lizards, amphibians and fish – and none of these groups is clade.

25. #25 Andreas Johansson

    April 11, 2008

    That makes a good case for a petition to make C. elegans the type species.

    I looked a bit further around, and it appears C. genitalis must be a later referal; according to the link at the end of this post, Caenorhabditis was created only in 1952 (originally as a subgenus of Rhabditis) for elegans and briggsae, and “maybe others”, implying one of those two must be the type.

    http://plpnemweb.ucdavis.edu/Nemaplex/General/Biographies/ECDougherty.htm

26. #26 Sven DiMilo

    April 11, 2008

    biologists de facto found clades useleless and don’t use them. We talk about great apes, elephants, artiodactyls, antelopes, raptors, lizards, amphibians and fish

    While I myself have argued repeatedly on various blogs that paraphyletic groups are useful informal concepts and need not be shunned (the classic example is “reptiles”), it’s going way to far to claim that “biologists have found clades useless and don’t use them.” Of course we use them! Hence awkward but common terms like “non-avian dinosaurs” etc. And almost everybody agrees that formal taxonomy (whether using Linnean ranks or not) should be based on clades. Sure things will have to get shuffled around as new information becomes available, but that’s far from “unscientific”–it’s basically what the philosophy of science is all about!

27. #27 Jerzy

    April 11, 2008

    Well, “non-avian dinosaurs” are reasonably common while awkward. Sometimes you hear “non-human apes” if primatologist wants to subtly remind us of likeness of our lower brothers.

    But who never heard of “non-snake lizards” “non-tetrapod fish” “non-mammoth elephants” or “non-whale artiodactyls”?

    In case of dinosaurs, most common approach is that you see the order of Saurischia. Then you descend into suborders, superfamilies and families of theropods… into Aves. Then a scientist is supposed within next second to have a quick memory wipe-out, or sort of change of The Matrix, and believe that Aves magically turned from family into a class with orders like Struthioniformes, Anseriformes etc.

    Isn’t it a bit ridiculous?

28. #28 David Marjanovi?

    April 11, 2008

    Well, perhaps best would be to redefine taxonomic units as “ancestor and some or all its descendants sharing common morphology”.

    This would prevent taxo-madness when distinctive group is found to be nested within uniform clade.

    This is completely impossible, because it is impossible to quantify “common morphology”. Exhibit A: the demise of phenetics.

    Note that clades-based approach inherently cannot produce stable and practicaly useful taxonomy. It is somewhat unscientific. No matter how well researched is a group of organisms and its evolution, its cladistic taxonomy is unknown.

    1) Yes! The phylogeny of life is unknown. That’s why we have to use science and cannot rely on authority! You have it backwards.
    2) There is no such thing as cladistic taxonomy. Cladistics is the method of phylogenetics; it has nothing to do with taxonomy (even though Hennig used it for taxonomy). You have confused cladistics with phylogenetic nomenclature.

    Perhaps it is worth remembering that biologists de facto found clades useleless and don’t use them. We talk about great apes, elephants, artiodactyls, antelopes, raptors, lizards, amphibians and fish – and none of these groups is clade.

    Biologists talk about clades all the time, because it’s impossible to do evolutionary biology without talking about clades — and it’s impossible to do anything reasonably large in biology without doing evolutionary biology!

    And when biologists say “fish”, that always means one of two things: spinosaur food, or Danio rerio.

    In case of dinosaurs, most common approach is that you see the order of Saurischia. Then you descend into suborders, superfamilies and families of theropods… into Aves. Then a scientist is supposed within next second to have a quick memory wipe-out, or sort of change of The Matrix, and believe that Aves magically turned from family into a class with orders like Struthioniformes, Anseriformes etc.

    Isn’t it a bit ridiculous?

    Ranks are a bit ridiculous, yes.

    You haven’t read anything on dinosaurs written in the last 15 years, have you? The people who work on dinosaurs pay, at most, occasional lip-service to ranks and don’t really ever use them. There are never enough of them anyway!

    And, BTW, I have seen tems like “non-ophidian squamates” and “primarily aquatic vertebrates” in the literature. You need to go out less. :^)

29. #29 Sven DiMilo

    April 11, 2008

    And when biologists say “fish”, that always means one of two things: spinosaur food, or Danio rerio.

    That was pretty funny, even though I’m the kind of biologist that usually means neither!

    I will also agree that ranks are a bt ridicuouls, and of all the ridiculous ranks, those used for birds have always been the most ridiculous.

30. #30 Andreas Johansson

    April 11, 2008

    What, anyway, makes non-ophidian squamates an interesting grouping? Why not non-pythonomorph squamates, or non-anguid lepidosaurs?

    I’m partly serious. I have a lot easier seeing why people would want “fish” (Pisces) as a taxon than “lizards” (Lacertila, I guess).

31. #31 Jerzy

    April 11, 2008

    Well, back to basics.

    People talk all the time about rather clearly defined groups with generally good agreement about morphology. Biologists need taxonomy to give them common reference of names. There is clear order in naming species and genera, which we talked about before and which considerably limits confusion. With larger groups, there is the same need of order, but there is none. Introducing c

    quote: “This is completely impossible, because it is impossible to quantify “common morphology”.”

    In most cases it is quite clear. I never seen much disagreement what is “a lizard” or “an ape”.

    quote: “1) Yes! The phylogeny of life is unknown. That’s why we have to use science and cannot rely on authority! You have it backwards.”

    Actually, phylogeny of life is in many cases well resolved. But with resolved phylogeny, you will have chaos when you want to write anything of practical importance using nomenclature based on clades. Try to give common description of Cetartiodactyla.

    quote: “Biologists talk about clades all the time, because it’s impossible to do evolutionary biology without talking about clades — and it’s impossible to do anything reasonably large in biology without doing evolutionary biology!”

    Actually, most biologist talk about morphologically defined groups. When you go to e.g. IUCN, you note working groups of things like “small Afrotheria” (resurgence of insecctivores) and “Elephants and rhinos” (resurgence of long-defunct order of Pachydermia).

    “You haven’t read anything on dinosaurs written in the last 15 years, have you? The people who work on dinosaurs pay, at most, occasional lip-service to ranks and don’t really ever use them. There are never enough of them anyway!”

    I read lots of the only dinosaurs anybody cares about, and ranks and cladistic confusion are of outmost importnace. Because amount of money dedicated to survival of any extant dinosaur depends greatly from if it is a subspecies or species.

32. #32 Andreas Johansson

    April 11, 2008

    I never seen much disagreement what is “a lizard” or “an ape”.

    In the later case, you cannot have been looking hard.

33. #33 David Marjanovi?

    April 11, 2008

    I’m partly serious.

    I’m entirely serious

    “lizards” (Lacertila, I guess)

    Lacertilia and Sauria. (Sauria would have priority, but the Principle of Priority only holds for the family-group and lower ranks in the ICZN.)

    Introducing c

    Yes?

    In most cases it is quite clear. I never seen much disagreement what is “a lizard”

    Some people include the amphisbaenians in Sauria/Lacertilia, others don’t…

    More importantly, when there’s little disagreement, this shows the existence of consensus — not what that consensus is built on! In this case, it’s just tradition. If you tried to define Sauria/Lacertilia as “everything with x % or higher similarity to Lacerta agilis“, you would fail. Inevitably.

    Try to give common description of Cetartiodactyla.

    Mesotarsal joint in addition to the usual mammalian joint between tibia/fibula and astragalus…

    “small Afrotheria” (resurgence of insecctivores)

    Not at all, no — Eulipotyphla is excluded.

    Also, while all rhino species and subspecies are endangered, there are rather large differences. I bet the same people who talk about “elephants and rhinos” (and perhaps tapirs and hippos, so as to complete Pachydermata…) one minute talk about the western white rhino, the African forest elephant, and the Javanese rhino the next.

    My point is that not everyone uses the same working groups. So why should anyone’s working groups be given official names? Why not reserve the official names for something more objective?

    Because amount of money dedicated to survival of any extant dinosaur depends greatly from if it is a subspecies or species.

    Most species concepts have nothing to do with cladistics.

34. #34 Jerzy

    April 11, 2008

    quote”My point is that not everyone uses the same working groups. So why should anyone’s working groups be given official names? Why not reserve the official names for something more objective?”

    Because biologists need and use official names of groups. They also need these groups to be clearly hierarchicaly ordered, have common characteristics from practical point of view and have names which are relatively consistent and reliable. The same goes for even more professionals working in biotechnology, fisheries and conservation.

    If anything, a small minority of people studying phylogeny should stop confuse the majority by hijacking taxonomy. Anyway, clades need no one-word name at all. They can be named by one common ancestor or by two most distant offspring. There is no point of using scientific names for clades.

    Note – I naturally agree that clades are (if well discovered) a biological phenomenon. Only that building taxonomic system where all groups are clades makes this taxonomy impractical. Because of sudden switches, creating many near-identical groups or groups containing wildly different organisms.

35. #35 Sven DiMilo

    April 11, 2008

    Here is a brand new article on these very issues. I’m not sure what it means, but there it is.

36. #36 David Marjanovi?

    April 12, 2008

    Because biologists need and use official names of groups. They also need these groups to be clearly hierarchicaly ordered, have common characteristics from practical point of view and have names which are relatively consistent and reliable. The same goes for even more professionals working in biotechnology, fisheries and conservation.

    But all those professionals need different groups!

    And all of them need clades much more often than many of them know. This is because nothing in biology makes sense except in the light of evolution and nothing in evolution makes sense without a good phylogeny.

    Anyway, clades need no one-word name at all. They can be named by one common ancestor or by two most distant offspring. There is no point of using scientific names for clades.

    We need to talk about phylogeny all the time. This gets much, much easier if we can name clade and if we can define those names.

    Remember how it works in rank-based (“Linnaean”) nomenclature: taxon names are defined by a type and a rank. Hominidae is the name of the family to which Homo belongs — and “family” is not defined, therefore you are allowed to use the name Hominidae for absolutely any grouping that contains (or is identical to) Homo. And indeed, you can easily find at least three different uses for Hominidae in the literature (even the popular literature).

    See? This is an additional source for instability that phylogenetic nomenclature lacks. Instability in phylogenetic nomenclature is only due to uncertainty in our knowledge, never to mood swings like “well, actually, they’re different enough to deserve separate families rather than subfamilies”.

    Here is a brand new article on these very issues. I’m not sure what it means, but there it is.

    That’s a very philosophical article that, frankly, is so boring that I didn’t manage to finish reading it.

    However, “people who read this article also read” this one, which is very relevant to this discussion. Do check it out.

37. #37 Randy

    April 12, 2008

    Darren;

    If you plan on addititonal blogging about varanids, getting hold of Pianka & King 2004 is a must (see http://www.iupress.indiana.edu/catalog/product_info.php?products_id=21751 )! I imagine its also quite affordable for those of you across the pond given the dollar/pound exchange rate these days.

    Its also worth checking out the two recent molecular phylogenies of Varanus, one by Ast in 2001 in Cladistics, and the other is Fitch et al. 2006 in Australian Journal of Zoology.

38. #38 John Scanlon, FCD

    April 14, 2008

    The most recent phylogeny reference (mentioned by Randy) is Alison J Fitch, AE Goodman and Steve C Donnellan (2006), A molecular phylogeny of the Australian monitor lizards (Squamata:Varanidae) inferred from mitochondrial DNA sequences. Australian Journal of Zoology 54, 253?269.
    I only found this recently and seemed to recall it was in Mol Phyl & Evol in 2007, so on reading Randy’s comment I started searching the AJZ site for another one. Very slow and inelegant access to issue listings on the CSIRO site, and then got zero search results on ‘Fitch’ and on ‘Varanidae’. So I post the full details in case anyone else is looking… and just by the way, I have the pdf >
    I was a little disappointed they didn’t have a stab at calibrating the molecular clock (only using relative rates), but it just rubs in the fact it’s time I published some of my Oligocene stuff…

39. #39 Andreas Johansson

    April 14, 2008

    Vaguely related: Y’dy at the bookstore I saw a coffe table type book called “The Great Big Book of Snakes & Reptiles”. Can’t help but wonder what definition, if any, of “reptile” they’re using …

40. #40 David Marjanovi?

    April 14, 2008

    Wow. If you find out, please let me know!

41. #41 windy

    April 14, 2008

    That reminds me of another book with an amusing name, although not for reasons of cladistics:

    “The great nature of Africa. From Kilimanjaro to Serengeti”

42. #42 daniel bennett

    June 24, 2009

    That picture of varanus rudicollis belongs to me, You’d better donate something quick. Or else