eFfing #FossilFriday: Subfossil lemurs

Hard to resist the headline, “Enormous underwater fossil graveyard found,” from the National Science Foundation. The NSF posts a video detailing the discovery of an underwater cave system containing “hundreds of potentially 1,000-year-old [lemur] skeletons…” in Madagascar. As a paleontologist, hearing about the discovery large numbers of ancient skeletons is musical, like hearing Love This Giant or the new T Swift for the first time.

Two lemur crania in an underwater cave on Madagascar. Photo from nbcnews.com.

Two lemur crania in an underwater cave on Madagascar. Photo from nbcnews.com.

It’s a pretty remarkable discovery – hundreds if not thousands of bones representing many complete skeletons of various extinct lemur species. And toward the end of the clip is a skull of a pretty badass looking big cat. The video shows piles of loose bones dredged up from the cave. These will reveal lots of information about the biology of these recently extinct animals, especially if researchers can keep associated bones together.

So what are these animals? Lemurs are one of the most primitive living types of primates – although they are relatively closely related to us humans, they retain many characteristics of ancestral mammals. I know it’s hard to believe this aye-aye here is more closely related to you than to rodents, but it is:

An aye-aye (Daubentonia madagascarensis) using its narrow and elongated middle finger to fish for for grubs inside a tree that it’s opened up with its teeth.

Lemurs are found only on the island of Madagascar, and over the past several millions of years they have diversified into the roughly 100 species inhabiting the island today. But even just a few thousand years ago, there were more kinds of lemurs. This includes Megaladapis, the large-bodied “koala lemur,” and Hadropithecus, whose skull bears a striking resemblance to the extinct hominin Australopithecus boisei. As  Laurie Godfrey says in the video, “two thirds of the animals that lived there only a thousand years ago are gone.” Humans are probably largely responsible for the extinction of many Malagasy lemurs in both the past and especially the present.

Much of the ‘fossil’ record for lemurs is recent by fossil standards, and so most specimens haven’t become fully fossilized. As a result, lemur paleontology is besprinkled with the term “subfossil,” indicating bones that are really old and belong to extinct animals, but don’t fit the technical definition of fossils. The lemur subfossil record has taught us a lot about the evolutionary history, adaptations, and recently even genetics of this primitive group of primates, as well as about the ecological history of Madagascar. It will be very interesting to see what new insights will come from the recently discovered scores of underwater skeletons.


(Figure 3 from Ryan et al., 2008. Scale bar is 1 cm)

The next big thing? Automated methods in biology, or "Hooked on phenomics"

“This is very beautiful. It is neat, it is modern technology, and it is fast. I am just wondering very seriously about the biological validity of what we are doing with this machine.” – Melvin Moss, 1967*

“This machine” to which Moss referred nearly 50 years ago was not a contraption to clone a Neandertal or a Godzilla-like MechaGodzilla, but a computer. Along these lines, a paper came out recently describing a new, automated method for analyzing (biological) shapes, and while I think the method is pretty sweet, I think future researchers employing it should keep Moss’s monition in mind.

Doug Boyer and colleagues (2011) present “Algorithms to automatically quantify the geometric similarity of anatomical surfaces.” It seems the main goals of the study were to make shape analysis [1] faster and [2] easier for people who don’t otherwise study anatomy (such as geneticists), making it possible [3] to amass large phenotypic datasets comparable to the troves of genetic data accumulated in recent years. Using some intense math that’s way over my head, the computer algorithm takes surface data (acquired through CT or laser scans) of a pair of specimens and automatically fits these forms with a “correspondence map” linking geometrically (and not necessarily biologically) homologous features between the two. It then uses the map to fit landmarks (a la geometric morphometrics) which are used to calculate the shape difference metric between individuals in the pairings.

See at the right just how pretty it is! The authors posit that this technique could be used with genetic knock-out studies to assess how certain genes affect the development of bones and teeth, or to model the development of organs. That certainly would be useful in biomedical and evo-devo research.

But while I appreciate the automated-ness of the procedure, I don’t think we can simply write off the role of the biologist in determining what features are homologous, in favor of a computer. The paper itself illustrates this nicely. The authors state that there is debate about the origins of a cusp on the molar tooth of the sportive lemur (Lepilemur) – is it the same as the entoconid of the living mouse lemur, or the enlarged metaconid of the extinct “koala lemur”? Their automated algorithm can map the sportive lemur’s mystery cusp to match either alternative scenario. It is the external paleontological and phylogenetic evidence, not the intrinsic shape information, that renders the alternative scenario more plausible.

So let me reiterate that I think this paper presents an important step for the study of the biology of form, or the form of biology. Automating the analysis of form will certainly expedite studies of large datasets (not to mention freeing up the time of hordes of research assistants). But I hope that researchers employing this procedure will have a little Mossian Angel (poor play on “guardian angel,” sorry) on their shoulders, reminding them that the algorithm won’t necessarily show them homology better than their own experience. And I hope all biologists have this Mossian Angel there, reminding them that even though this method is “neat … modern technology, and … fast,” it may not be the most appropriate method for their research question.

Boyer, D., Lipman, Y., St. Clair, E., Puente, J., Patel, B., Funkhouser, T., Jernvall, J., & Daubechies, I. (2011). Algorithms to automatically quantify the geometric similarity of anatomical surfaces Proceedings of the National Academy of Sciences, 108 (45), 18221-18226 DOI: 10.1073/pnas.1112822108

*This quote comes from a discussion at the end of a symposium: Cranio-Facial Growth in Man (1967). RE Moyers and WM Krogman, editors. New York: Pergamon Press.