Taxonomy can trace its roots back to the work of Linnaeus, who, working from a distinctly Creationist perspective, sought to classify the living world.  However, much has changed since his time.  Darwin published the Origin of Species in 1859, and his work suggested the plausibility of an updated system for classification.  Today, we have such a system.  Cladistic analysis is a newer system of classification (popular in the last 50 years) that has taken hold in recent years.  In fact, it is the basis for the structure of the American Museum of Natural History’s paleontology displays, and is incorporated into the instructive framework of paleontology displays in many other museums.   Let’s take a look at how the system operates.

The taxonomic structure of a cladogram is based on ancestry; a good, monophyletic clade (group sharing same ancestry, see Holtz and Brett-Surman, 92-106) includes only a common ancestor and its descendents.  For example, a Ceratopsian cladogram might include Psittacosaurs and other basal ceratopsians, as well as Protoceratops and more advanced ceratopsians such as Triceratops.  But how is ancestry defined?

Cladistic analysis focuses on shared derived characteristics to identify relationships.  For example, a relatively simple cladogram for humans could include the following traits:

1) presence of a notochord, placing humans within the Chordates.
2) presence of a backbone, thus rendering humans vertebrates.
3) presence of an amniotic sac, rendering humans amniotes.
4) (skipping a bunch here) presence of mammary glands and hair, thus rendering humans mammals
5) presence of a placenta, thus rendering humans placental mammals…

As you can see from the simplified illustration above, cladograms move from basal (or “simple” or “common”) traits towards derived characteristics, such as the placenta. There are more derived characteristics (obviously) defining the human species’ position in a taxonomic hierarchy, but I simplify here for sake of space and in an attempt to prevent complete boredom on the part of a casual reader.  A good cladogram always moves from least specific to most specific with regards to shared characteristics.  If a relationship fails the test of shared basal characteristics, then any apparently “derived” characteristics must be the result of convergent evolution.  Take, for example, birds and bats.  While both fly, birds have feathers and other distinctly archosaurian features, while bats exhibit distinctly mammalian features.  Therefore, birds and bats do not comprise a monophyletic clade. 

One of the key attributes of cladistic analysis is the fact that it can predict the presence of ancestral species even when we have no record of these species. For example, in the case of Archaeopteryx (and birds in general), almost all paleontologists would agree that these organisms are best classified as derived maniraptors.  The presence of many transitional features within Archaeopteryx (bony tail, claws, teeth, hip structure, neck shape, etc.) confirm this model, showing that Archaeopteryx, as a bird, had a demonstrably dinosaurian ancestry, specifically placing Archaeopteryx within a very specific branch of theropod dinosaurs, the maniraptors.  In instances where we cannot trace every transition in form from basal maniraptors into Archaeopteryx, scientists can infer the likely transitions that took place.  This is possible due to the fact that cladistic analysis focuses only on features unique to a single group within a clade. Thus, when antievolutionists claim that Archaeopteryx is nothing more than a “mosaic form” like the platypus, they are misrepresenting science.  Archaeopteryx’ features are transitional from a cladistic perspective, with features “in-between” that of basal theropods and modern birds, thus rendering Archaeopteryx a valid confirmation of evolutionary theory.  Archaeopteryx shares both basal and derived features with birds, thus passing the test of cladistic analysis.  The platypus, on the other hand, while having webbed feet and a bill, does not pass the key tests for “birdiness” (please note that this term is inherently unscientific, and is being used only for ease of explanation) such as presence of feathers, hollow bones, etc.  The basal features of the platypus place it on a basal tree of mammalia. 

Occasionally, Creationists will also use the claim that “since we can’t prove that a fossil reproduced, this means that it is not a valid transitional fossil”.  This is also a misrepresentation of how scientists think about ancestor-descendent relationships.  The search for transitions is not for transitional forms, but rather transitional features (as highlighted in Padian and Angielczyk, 197-231).  Thus, in the case of Archaeopteryx, to quote Padian and Angielczyk:

The point that we emphasize here is that the “bird” and “reptile” features of Archaeopteryx, or any such animal, can be explained in quite orderly fashion with  reference to their distribution on a cladogram… This distribution makes sense because it shows when each feature arose and was passed down, often in modified form, to the descendants of the first animals that had it.” (Padian and Angielczyk p. 209)

As demonstrated by the above quote, while Archaeopteryx has the characteristics to stand alone as a good piece of evidence for evolution, it is only in context where its significance truly makes sense.  If somebody asks for “just one transitional fossil”, as Creationists often do, they are misunderstanding how paleontology and taxonomy truly operate.  Through the use of cladistic analysis, scientists can pinpoint exact transitional features in context, rather than in a vacuum.  Nothing in evolution makes sense without context.  You cannot claim that a derived characteristic is transitional between two organisms if these organisms do not share the most basal characteristics on a cladogram.  Cladistic analysis always works from basal towards derived, so by the time one is ready to highlight “transitional features”, there is already a solid body of evidence to demonstrate a close relationship between the organisms in question.  It’s not just one isolated feature that’s important; it’s the sum of all parts.  Even while there are gaps in the fossil record, cladistic analysis allows to infer what is missing in these gaps, and even to predict what type of organism to expect in these gaps.  If you want to demonstrate to yourself that this process works, look up early amphibian evolution, remove any information on Tiktaalik rosea (to create a gap for yourself), and predict what type of transitional forms you would expect to appear in filling this gap.  Then compare your prediction with Tiktaalik’s description.  If you’ve developed a good prediction, it should line up pretty closely with the actual specimen.
Works Cited:
Holtz, T. and Brett-Surman, MK. The Taxonomy and Systematics of the Dinosaurs. In The Complete Dinosaur, ed. Farlow, JO and Brett-Surman, MK, Indiana University Press, Bloomington, 1997, p. 92-106.
Padian, K. and Angielczyk, KD.  “Transitional Forms” versus Transitional Features. In Scientists Confront Creationism: Intelligent Design and Beyond, ed. Petto, AJ and Godfrey, LR. WW Norton & Company, New York, 2007, p.197-231.

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7 Comments on “cladistics”

  1. johnG Says:

    Thanks for addressing this topic. I’m afraid it’s still too abstract for me to understand what is the difference between cladistics and what was used previously. I took some botony classes 25 years ago that taught me to view taxonomy in terms of evolution and derived traits. I started hearing of cladistics within the last ten years, and that cladistics offers the means of making testable predictions. I see that point made nicely in your last paragraph, but I still don’t know what is new and different about cladistics.

    I’m not citing a deficiency in your writing, rather, I’m sharing my own lack of understanding. Unlike you, I only sample parts of the modern literature and try to connect it with training from years ago. I don’t have the benefit of being immersed in an academic setting and the current thought that comes with it.

    I enjoy your writing.

    John Garrett

    • Carissa Madsen Says:

      I find that pictures help with understanding cladistics and taxonomy. I found the following website which covers cladistics and Linnaeus with pictures included:
      No offense to the author for not having pictures, I understand copyright laws, formatting and time/space constraints.

    • darwinaia Says:

      I’m not always the best on clarity with things. Just looked around for some other sources on the topic. The Talk Origins site has a pretty good thing on it ( here: ). Their site tends to focus on the creation-evolution stuff generally, but it has some pretty good articles/details. I’ll look around for some more historical stuff on cladistics as well. I’ll put a section for sources on cladistics up with my links as well.

      Relatively random sidenote off of your reply (inspired by your mentioning of botany). I’m not sure if you’ve seen it (it’s one of his lesser-known works), but Darwin actually published a book on carnivorous plants (available here: ). Shows yet another side of the guy’s work.

      Glad to see you enjoy my writing by the way. Thanks for taking time to read my posts; it helps knowing that people are actually enjoying them.


    • johnG Says:

      Thank you both for your comments and references. I did a quick skim of the links and will have to study them in more detail, but I think I understand it: whereas traditional taxonomic categories may follow evolutionary paths, that is not the emphasis; it’s more about sorting the species into managable pages within a book. I see in cladistics the effort to figure out which traits represent evolutionary branching and the taxonomy is sort of an overcoat, a set of labels but not the emphasis. I guess another way to look at it, cladistics represents a living line of inquiry toward the evolutionary relationships being analyzed. Does that sound right?

      Regarding pictures and respect for copyright, I’m an illustrator, so it would be a pleasure to collaborate on an illustration if you need one. You can follow my name link and see some samples from my website’s home page.

      You mentioned carnivorious plants. This is a fascinating topic and comes up a lot in educational projects I’ve worked on. It never ceases to amaze me what Darwin studied. What did he have to say on flight? I’m currently fascinated by the independent evolution of gliding or flight: e.g, squirrels, bats, pteronodons, insects, frogs (gliding on webbed feet), lizards (using elongated ribs), and even a species of asian brown snake that flattens its body and ungulates, achieving more distance than otherwise when swinging between trees.


      • darwinaia Says:

        Yeah; sound’s like you’re got the key thing with the cladistics stuff. A lot of it is an attempt to derive an evolutionary-based scheme. Evolutionary relationships are a strong emphasis in the system, pretty much the major one. Just went back through some of my old books from class this morning. One of the books from a Museum History course I took a few semesters ago sums up the distinction while discussing the use of cladistics at the American Museum of Natural History (wish I had remembered it when I did the post):

        “The cladistics school of taxonomy, which outlived phenetics and became the basis for the floor plan of the AMNH, takes a very different approach. Cladistics attempts to group taxa hierarchically, based on shared derived characters (hypotheses of homology). Unlike the pheneticists, many cladists interpret their classification patterns to represent genealogical relationships. All the members of a taxon must have a common ancestor.” (Asma, ST. Stuffed Animals and Pickled Heads: The Culture and Evolution of Natural History Museums. Oxford University Press, Oxford, 2001 p. 182).

        Note that cladistics essentially replaced phenetics.

        Sweet website by the way. I especially like your geologic timeline. I’m going to link it with the paleontology links on my blog. Hope you don’t mind. Your “Earth, Orbit, and Climate” stuff is nicely done as well. Thanks for the offer to work with illustration as well; I’ll have to keep that in mind. You’re definitely good with it, so I’d be interested in working with you at some point.

        Darwin seems to touch upon a lot of major issues today in the Origin of Species. One of them actually is flight. Darwin offers a pretty interesting explanation(I’m working with a facsimile that’s pretty much an exact copy of the original from Harvard University Press, p.180-2). He suggests the flight membrane in bats as a possible offshoot of membranes used for gliding (especially in Galeopithecus, the flying lemur). He discusses squirrels previously (on 180), and uses a scope from non-gliding squirrels through gliding squirrels, essentially hinting at the evolvability of gliding as well. On 182, he offers an interesting observation:

        “Seeing that a few members of such water-breathing classes as the Crustacea and Mollusca are adapted to live on the land, and seeing that we have flying birds and mammals, flying insects of the most diversified types, and formerly had flying reptiles, it is conceivable that flying fish, which now glide far through the air, slightly rising and turning by the aid of their fluttering fins, might have been modified into perfectly winged animals. If this had been effected, who would have ever imagined that in an early transitional state they had been inhabitants of the open ocean, and had used their incipient organs of flight exclusively, as far as we know, to escape being devoured by other fish?”

        I like that paragraph because it essentially chastises people who would be against the evolveability of flight for having a lack of perception or imagination. The discussion of flight is in every edition of the Origin if I’m not mistaken. Flight is an interesting topic; it’s intriguing that its evolved so many times independently. Definitely shows the shaping power of convergence in evolution.


  2. johnG Says:

    Thank you first for helping me sort out “cladistics”. That’s been on my to-do list for some time, and thanks again for linking to my site. As viewed from my end, the text is running off the page, so please feel free to shorten the label to Geological Timeline or Interactive Geological Timeline, whatever fits. Don’t mess up your nice page.

    I have your blog linked on mine–shouldn’t impact your traffic stats any 🙂


    • darwinaia Says:

      No problem; glad to help! You’ve probably got the predictive ability of cladistics down as well; with the focus being placed on actual evolved linaeages, one can predict what intermediate features should exist between species A and species C, thus giving a good likely picture of what species B, right between the A and C, looks like. It’s pretty neat to look at.

      Thanks for both the link to my page and for letting me know about the text on the link to yours. Just fixed that. I like your timescale setup; more detailed than many yet still easily accessible to the average reader. I like your layout for it especially, starting with a relatively basic timescale and then getting more detail as you click into the different divisions. Makes it useful for both quick and also relatively more detailed reference, rather than one or the other.


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