02 January 2013

All Known Great Ape Individuals (Messinian to Present)

Happy 2013, everyone!

Recently I announced a code package I was working on, called Haeckel, for generating vector-based charts related to evolutionary biology. Here's an image I've created using it:

Known Great Ape Individuals
This chart represents all known hominid individuals (Hominidae = great apes, including humans and stem-humans) from the Messinian to the present, erring on the conservative side when the material is too poor to determine the exact number.

If you've been following this blog for a few years you may remember an earlier version of this. I've done a lot of refinement to the data since then. The earlier versions were dissatisfying to me because the horizontal axis was essentially arbitrary. For this version I used matrices from a phylogenetic analysis (Strait and Grine 2004, Table 3 and Appendix C) of craniodental characters to generate a distance matrix, and then inferred positions for other taxa based on phylogenetic proximity and containing clade. This is similar to the metric I used in this chart, except that it incorporates Appendix C, uses inference, and averages distance from humans against distance from [Bornean] orangutans. Don't be mistaken  this is still arbitrary. But it's a bit closer to something real.

Stray notes:
  • I'm pretty sure there are Pliocene stem-orangutans somewhere, right? Might have some work left to do on that data.
  • The dot with no taxon above "Australopithecus" is an indeterminate stem-human from Laetoli. It should probably go further left.
  • The Ardipithecus bubble includes the poorly-known "Australopithecus" praegens. (Although in some runs it moves outside  there's a random element to the plotting.)
  • The Holocene is barely visible up at the top. What a worthless epoch.
  • Homo floresiensis (hobbits) are far to the left of Homo sapiens because I placed them outside Clade(Homo erectus  Homo sapiens).
  • You may recall Lufengpithecus? wushanensis as "Wushan Man", as it was originally placed in Homo erectus. (Hey, it's just teeth.)
  • A couple of fossil chimpanzees, lots of fossil orangutans, but no fossil gorillas. :(
    • (Unless you count Chororapithecus, but that's pre-Messinian. Very pre-Messinian. Suspiciously pre-Messinian....)
  • Look at all that overlap between Homo, Paranthropus, and Australopithecus!
    • I have a feeling, though, that if I added another dimension, Paranthropus and Homo would jut out in opposite directions.
    • Reclassifying Australopithecus sediba as Homo sediba would also decrease the overlap. (Although its position is inferred  actually scoring it might do the same thing.)
    • It's frustrating that the type species of Australopithecus and Paranthropus are also just about the most similar species across the two genera.
  • Kenyanthropus and Praeanthropus have been provisionally sunk into Australopithecus.
  • Should we just sink Orrorin and Sahelanthropus into Ardipithecus? Why not?
  • My guess is that if I added postcranial characters, the stem-humans would all shift right (humanward). Oh, for a good matrix of postcranial characters....
Oh yeah, and if you want a peek at the data, go here.


  1. This is great. I find myself yearning for hover-over meta-data (locality, elements, classification history) but that's probably asking too much.

    "The Holocene is barely visible up at the top. What a worthless epoch."

    Where's the Anthropocene? [kidding]

    "A couple of fossil chimpanzees, lots of fossil orangutans, but no fossil gorillas. :("

    see dumb joke on Twitter

    "Should we just sink Orrorin and Sahelanthropus into Ardipithecus? Why not?"

    For that matter, what's to distinguish all of these from (Pliocene at least) Australopithecus? More seriously, is there a rationale behind the dotted genera boundaries?

    1. Is there ever a rationale for generic boundaries?

      I could easily do a hover-over bit when I'm done.

    2. Hmmm...

      With that in mind I would vote to ditch the dotted polygons altogether. Things like the apparent morphological bottlenecks in the Ardi and Chimp polygons raise questions: is that a real evolutionary pattern or just a sampling artifact (I'm guessing the latter).

      Color-coding the genera could be a better option? Plus that would clarify who is who in the areas where the genera boxes overlap. (Although that hover-over idea would take care of this as well).

      Not that you were looking to workshop this, just my 2c. as someone who would probably love to use this for teaching down the road.

    3. (Yes, it's a sampling artifact.)

      I prefer to keep this black and white for a couple of reasons (easier to publish, less trouble for color-blind people). But I could try a version with symbols (e.g., Xes for Homo, squares for Australopithecus, etc.)

      Workshop comments are entirely appropriate!

  2. Chororapithecus is doubtfully related to the Gorilla-lineage. The available evidence does not rule out that its reported similarities are the result of homoplasy.

    Australopithecus sediba is currently still of uncertain placement. I have heard some researchers say that it should be in Homo, but they are cautious about stretching the definition of what genus constitutes. Dr. Bernard Wood remains unconvinced of its separate species-status and argues that it may be distinct from one population of A. africanus, but that the authors did not sufficiently distinguish it from others. Stw505 and Stw53 are good examples of the variability of A. africanus. Further study of the variability of South African Australopithecus is necessary to argue the case one way or another.

    Kenyanthropus differs from Australopithecus in quite a few ways. You don't have to take my word for it, but there is a good, fairly recent paper by Spoor et al. arguing the case for a separate generic identity for the Kenyan taxon.

    The Ardipithecus-Orrorin-Sahelanthropus taxonomic debate cannot be resolved at the moment based on the limited amount of data available for the latter two taxa. People have their reasons for arguing one way or another. Honestly, I am not even sure if the two Ardipithecus species belong together in a single genus, as the proposed genus diagnosis includes several homoplastic and/or more broadly distributed traits (e.g. canine reduction). On the other hand, I am interested in learning why you opt to place them all together in a single taxon: Ardipithecus.

    1. Because genera are BS anyway I mean, look at the pongine genera: some of them (Gigantopithecus and perhaps Lufengpithecus) span half the Neogene + Quaternary. Meanwhile, in the human total group, half the species get a genus according to someone. If kadabba, ramidus, tchadensis, and tugenensiswere pongines you know they'd all be in one genus.

      I'll check out the Spoor paper. But again, genera are BS. (And it's not like I sunk platyops into afarensis.)

    2. A. sediba was compared to StW 53 in the original paper. They found StW 53 to be the sister group to Clade(HomoA. sediba). See my earlier post.

  3. I'm a total lay person here, and not quite sure how to interpret this thing. Are you plotting individuals by morphology and time, and then post-stratifying them into genera, or are the genera on the chart based on what was originally assigned to the individuals? If it's the latter, how can dots fall into more than one genera?

    Or am I totally misunderstanding the project? (Which I suspect is most likely.)

    1. Are you plotting individuals by morphology and time

      Yes. That is the primary purpose. The generic regions are just for labeling purposes, and are not based on anything scientific. As I've said before, genera are just bookkeeping bins.

      Dots can fall into more than one genus because I'm compressing the morphological disparity into a single axis — a massive simplification. So, e.g., Sahelanthropus tchadensis and Paranthropus boisei are around the horizontal center because their skulls and teeth are about as similar to those of orangutans as they are to those of humans (according to the matrix). But that doesn't mean they are exactly alike. Tyrannosaurus rex would probably end up there, too, since it's just as much like an orangutan as it is like a human!

  4. lots of fossil orangutans

    Another total layperson here: Did somebody decide that Sivapithecus was invalid or off the Orangutan line while I wasn't looking?

    1. Still considered a stem-orangutan, but it's too early to appear on this chart.