I think about extinction a lot. Its hard not to when researching Pleistocene mammals. One of the sobering things about this kind of research is that you become aware of the high likelihood of “unknown unknowns”: animals that existed but left no fossil traces for us to find, no hard evidence to let us know of their time on this planet. The scores of species that are known from just one fossil site, or just a few scraps of unusual bone all but confirm that there must have been species that we will simply never know about. And mammals are the one animal group that we actually have a good handle on. Think about how many Pleistocene fish, insects, and other groups we are likely to have missed.
In these kind of situations it is the insular, endemic, and highly specialised fauna of island ecosystems that are most likely to have been totally erased, given they are generally low in population size and restricted in range. It makes it all the sweeter when incredibly rare fossil island taxa get scientific (or media) attention. I would like to introduce a taxon known from only a handful of fossil sites, which comes from the island of Madagascar, and went extinct in the late Holocene. The unique bibymalagasy (Plesiorycteropus madagascariensis) is incredibly weird.
Despite being practically next door to Africa, Madagascar’s fauna is stuffed full of weird endemic creatures: the lemurs, the elephant birds, the eupleridae. The Mozambique channel is so strong that almost nothing gets to Madagascar from Africa- even humans colonised it from the East (the native Malagasy are thought to be a Bornean diaspora). When familiar creatures did arrive from Africa (like the hippos), they evolved in strange directions (into dwarf hippos, with large floppy ears according to local folklore). If selection pressures are intense, issues of homoplasy can come into play, and given enough time, the true ancestry of a species can be obscured. This seems to have been what happened with the bibymalagasy (the name simply means “Malagasy animal”).
Originally described as a relative of the African aardvark (Orycteropus afer) in the 19th century, this dog-sized mammal would surely have continued to be neglected by science if it wasn’t for the attentions of one determined researcher. Ross MacPhee of the American Museum of Natural History gave a comprehensive overview of Plesiorycteropus in 1994, surveying all known material (and erecting a new species P.germainepetterae for some of the material). In his scholarly work, MacPhee argued that almost all the characters that had been used to group the bibymalagasy with the aardvark were as a result of strong convergent evolutionary pressures for a similar insect-eating and burrowing way of life. The super-strong digging arms, the lack of teeth in the mouth (a guess, as no fossil mandibles or maxillae are known), had obscured the true ancestry of the bibymalagasy, and it instead needed the creation of its own order, the bibymalagasia!
Here is how things would have stayed, barring the discovery of new, more complete bibymalagasy material until a really shocking paper came out in 2013.
In parallel to the well-known history of getting ancient DNA from extinct mammals, researchers in York, Manchester, and other centres have pioneered the process of getting protein from subfossil bones. Whereas DNA is quite an unstable molecule and breaks down rapidly after death, except in special circumstances (think the freezer-like conditions of the Beringian permafrost), protein often fills the role of biological building material and some proteins (e.g. collagen, keratin) can last for thousands or perhaps millions of years. In an analogous way to DNA, proteins can be sequenced and the sequences used to build phylogenies. Although all attempts at getting ancient DNA from Plesiorcyteropus have failed, partly due to problems with preservation and partly due to the difficulty of designing good molecular probes for something as supposedly isolated on its own branch of the mammalian tree, Dr Mike Buckley managed to get ancient protein from a few grams of precious bibymalagasy bone. And what did those sequenced fragments of collagen show? The completely unexpected grouping of Plesiorycteropus with the Tenrecidae– the superficially hedgehog-like mammals that find their greatest diversity on Madagascar.
Using cutting edge techniques, Mike has solved a century-old enigma. Plesiorycteropus was a tenrec that had taken up a myrmecophagous lifestyle, and the needs of its lifestyle had so altered its body that its tenrec origins had been almost completely obscured. Except in the microscopic molecules that made up its bones!
Written by Ross Barnett (@DeepFriedDNA)
Protein- Protein is what DNA codes for within the cell. The three letter code that DNA is written in acts as a template for the organisation of a string of amino acids into a chain. A chain of amino acids is a protein, and they make the organism’s metabolism work by providing enzymatic catalysts, structural support, transporter molecules, anything! If a growing organism is a bit like a lego set, then DNA is the instruction book and amino acids are the bricks.
Collagen- A structural protein made up mostly of the same repeating set of amino acids that has a triple helical structure giving it great strength and flexibility. Found in bones and cartilage, amongst other tissues.
Keratin- Another structural protein that forms helices and is the main component of skin, hair, and nail.
Homoplasy- When creating a phylogeny or family tree it can be difficult to decide what characters are important due to shared ancestry and which are evolutionary innovations. For example, lions and cows have tails with a tuft of hair on the end, but this character does not indicate recent common ancestry, it is a feature that has been derived independently. Tufted tails in lions and cows is a homoplasy. Since phylogenies are built by comparing a whole suite of character traits amongst a range of taxa, if homoplasies are used, then the resulting tree will be nonsense.
Buckley, M. “A Molecular Phylogeny of Plesiorycteropus Reassigns the Extinct Mammalian Order ‘Bibymalagasia’.” PLoS One 8, no. 3 (2013): e59614.[Full Text]
Burney, D. A., and Ramilisonina. “The Kilopilopitsofy, Kidoky, and Bokyboky: Accounts of Strange Animals from Belo-Sur-Mer, Madagascar, and the Megafaunal “Extinction Window”.” American Anthropologist 100, no. 4 (1999): 957-66.[Abstract]
MacPhee, R. D. E. “Morphology, Adaptations, and Relationships of Plesiorycteropus, and a Diagnosis of a New Order of Eutherian Mammals.” Bulletin of the American Museum of Natural History, no. 220 (1994): 1-214.[Full Text]