Sunday Primate: Kipunji (Rungwecebus kipunji)

Rungwecebus kipunji is an old world monkey native to Tanzania. It was first described in Science in 2005 (Jones et al., 2005). Although it was known to the people who lived around Mount Rungwe by the name "Kipunji", the existence of this species had not previously been documented in any scientific literature. Some researchers working in the area originally believed that Kipunji was what the locals referred to as a "spirit animal" and doubted its actual existence. This of course changed when they able to observe it and photograph it in the wild.

Photo from Save Our Species.

Based on appearance Jones et al. (2005) initially described Kipunji as a type of mangabey and gave it the name Lophocebus kipunji. Like other mangabeys, Kipunji is arboreal and has non-constrasting black eyelids. It can be distinguished from previously known species by an upright crest, off-white tail and a very district vocalization (sometimes referred to as a "honk-bark").

Shortly after the publication of Jones et al. (2005), a Kipunji specimen was discovered in a trap by a local farmer. This allowed scientists to conduct a more rigorous examination. Surprisingly, although it shared many morphological characteristics with mangabeys (genus: Lophocebus), mtDNA comparisons showed that Kipunji was more genetically similar to baboons (Papio) and gelada monkeys (Theropithecus). Keeping Kipunji in the same genus as the other mangabeys would have turned Lophocebus a paraphyletic clade. As it does not posses the same morphological features of other members of the Papio genus, it was decided that it should be placed within it's own genus. It was then given the name Rungwecebus kipunji. The publication of these findings by Davenport et al. (2006) marked the first time a new genus of monkey was described since Allen's Swamp Monkey in 1923.

As Kipunji is such a newly discovered species, not a whole lot is known about it. It is found in two isolated forests, the Ndundulu forest and the Rungwe-Livingstone forest in Tanzania. In total there are only about one thousand individuals alive today and it is classified as a critically endangered species. Tanzania has recently declared the Ndundulu and Rungwe-Livingstone forests as nature reserves in order to help protect Kipunji and other endangered fauna from extinction. For more info on Kipunji conservation efforts see Save Our Species.

Photo from Smithsonian.

This is the first time I've done a Sunday Primate in sometime. I hope to make it a regular occurrence once again. I'm taking suggestions. What's your favorite primate? Here's a list the previous installments in this series. I think this is most of them, but I know it's missing a few.

Previous Sunday Primates:
Pan troglodytes - January, 24, 2009.

Tarsiidae - February 7, 2009.
Hylobatidae (Gibbons) - February 14, 2009.
Macaca fuscata - February 22, 2009.
Nasalis larvatus - March 1, 2009.
Aegyptopithecus - March 7, 2009.
Saguinus imperato - May 10, 2009.
Galago - June 14, 2009.
Gorilla - September 6, 2009.
Saimiri - September 13, 2009.
Aotus - September 19, 2009.
Rhinopithecus roxellana - April 25, 2010.
Nycticebus - May 2, 2010.
Lemurs (general) - May, 10, 2010.
Therapithecus gelada - May 30, 2010.

Next week: Allen's Swamp Monkey (Allenopithecus nigroviridis)

Blog Clog

There's been a ton of exciting paleontological papers published within the past month that I've been meaning to write about: early Miocene cercopithecoids and hominoids, new australopithecine isotope studies, turtle shell evolution, and so on.

What have I been doing? Digging 1x1 m holes in the southern Ontario landscape, playing a bit of rock and roll,  and reading a book on human evolution that was last published in 1963. Additionally, my primary computer had a major malfunction and needed to be returned to the manufacturer. Thankfully, I was able to retrieve all my writing and data from the past five months. I think the new computer will arrive sometime late this week (or more likely early next week). At that time I'll be back to regale you all with my half-informed opinions on the aforementioned scientific discoveries.In the meantime here's a young gorilla and a young chimp hanging out together.

Photo by Michael Poliza.

FUCKHAWK

Here's a new website I put together: fuckhawk.tumblr.com . It is the internet HQ of my new punk rock band: FUCKHAWK. It's in capital letters because I'm screaming it at you. If you're in Toronto this summer and you like short, fast, punk rock, come see us play. We will be at the Bovine this Tuesday (May 29, 2013) and likely other Tuesdays throughout the summer. I'll also be adding more videos over the next few weeks. Yeeeooooowwww!

Did you hear they found some Pliocene hominin ear bones?

In a new PNAS paper Rolf Quam and colleagues describe the ear bones of two South African Pliocene hominins,  Paranthropus robustus (2.0 - 1.2 MA) and Australopithecus africancus (3.3 - 2.3 MA). Ear bones are pretty fricken hard to find, even in recent historical burials. These are pretty awesome discovery.

A little backstory:

Some paleoanthropologists argue that robust australopithecines ( or Paranthropuses as I inaccurately like to call them) form unique clade of relatively large-boned, big-jawed, bipedal hominins which diverged from the gracile australopithecines over two million years ago. This clade includes P. robustus, Paranthropus boisei, and Paranthropus aethiopicus. Others argue that P.robustus and A. africanus are more closely related, forming their own unique South African australopithecine clade. In this view the cranial and mandibular morphological similarities between P. robustus, P. boisei, and P. aethiopicus are thought to homoplasies (i.e. convergent or parallel evolution). One suggestion is that the paranthropuses were hard-object feeders and that their similar diets produced their similar jaw structure. The current consensus, however, which is based upon multiple cladistic analysis, does seem to suggest that the Paranthropuses form their own monophyletic clade (check out his article by Paul Constantino out for more details)

Into the ears:

This new study by Quam et al. (2013) does not about answering any of these long lasting cladistic disputes. It's really about looking at the differences and similarities between the ear bones of these pliocene hominins, modern humans, and chimpanzees. The inner ear is composed of three bones: malleus, incus, and stapes. The authors show that the morphology of P. robustus and A. africanus malleus more closely resembles that of a modern human, whereas the incus and stapes more closely resemble that of an African or Asian ape. Quam et al. (2013) argue that the change in malleus shape has a deep phylogenetic origin and that "and this may represent one of the earliest human-like features to appear in the fossil record" (Quam et al., 2013: 1) 

I think that's a bit of a stretch. Remember these ear bones come from a fossil which is 2.0 years old. The oldest bipedal hominin, Sahelanthropus tchadensis, dates to 7.0 MA. That means there's a 5 million year gap after the initial occurence of bipedalism and these particular P. robustus inner ear fossils. Although Quam et al. (2013) show that the P. robustus malleus is substantially different (and more human-like) than a chimpanzeee malleus, this change could have happened just about anywhere in the 5 million gap.

Furthermore, the incus and stapes look very chimpanzee-like. This means that these two bones evolved only changed shape to become more human-like sometime after 2.0 million years ago. Thus, if only 1/3 of these bones can said to closely resemble a modern Homo sapien ear bone, and the first known appeareance of this particular morphology occurs 5 million years after the initial appearance of bipedalism, you don't know how deep their phylogenetic origin.

There are much earlier hominins like S. tchadensis, Orrorin tugenensis, Ardipithecus ramidus, Ardipithecus kadabba. We know nothing about the shape of their inner ear bones right now. We won't until fossils of their inner bones are found. If it turns out their malleus is more human-like than chimpanzee-like, then we can say that this change is a definitively early hominin trait and a deep phylogenetic origin. Until those discoveries are made I feel that this particular claim of Quam et al. (2013) is a bit premature.

Jeesh, do I sound like a curmudgeon or what? Don't get me wrong, I still think this find is awesome, super important, and extremely informative. I just don't think there is sufficient evidence to say these particular changes in the inner ear have "a deep phylogenetic origin". That is all.

What did they hear?

That's pretty hard to say, but Quam et al. (2013) suggest that the differences in australopithecine/paranthropus inner ear morphology would have given them different auditory abilities. That means the range of hearing, as well as the actual sounds being heard, could have been quite different for these species (as compared to modern humans). There's definitely more work to be done in this regard, and I'm excited to hear more about it.

• Quam, R.M. de Ruiter, D.J., Masali, M., Arsuaga, J-L, Martínez, I. Moggi-Cecchii, J. 2013. Early hominin auditory ossicles from South Africa. Proceedings of the National Academy of Sciences. Early Online edition.

Junk DNA, biological function, and Utricularia gibba

DNA codes for proteins, or at least some of it does. In humans only about 2% of an individual's DNA actually codes for proteins. That means 98% of your genome is non-coding DNA (aka junk DNA). What does this non-coding DNA do? Some of it serves a structural purpose, some of it plays a role in regulating DNA transcription and translation, but most of it does not appear to have any biological function.

Enter the ENCODE project (Encylopedia of DNA Elements). In the fall of 2012 some 30 papers were published in journals like Science and Nature by members of the ENCODE project in which the authors suggested that approximately 80% of the human genome serves some biochemical purpose/biological function. This prompted Science writer Elizabeth Pennisi to write the following Eulogy for Junk DNA:

"Beyond defining proteins, the DNA bases highlighted by ENCODE specify landing spots for proteins that influence gene activity, strands of RNA with myriad roles, or simply places where chemical modifications serve to silence stretches of our chromosomes... The ENCODE effort has revealed that a gene's regulation is far more complex than previously thought, being influenced by multiple stretches of regulatory DNA located both near and far from the gene itself and by strands of RNA not translated into proteins, so-called noncoding RNA."

Following this, a number of scientists published response papers criticizing the ENCODE project (here's four). To the best of my understanding this debate centers around the idea of what constitutes "biological function". The Nature ENCODE papers seemingly used a different definition of "biological function" than what is accepted by most biochemists/geneticists.

Whenever I talk about DNA I'm paranoid about getting something wrong. It's not my field of specialty. Most of my knowledge comes from an undergrad genetics course, an undergrad organic chemistry class, and a small handful of journal articles and books I've read in my spare time. Oh, yes, and course the blog of University of Toronto biochemist Larry Moran: Sandwalk. Moran, like many other biochemists, has been fairly critical about the claims of the ENCODE project. Last September, he wrote the following response to Pennisi's Eulogy:

"Many scientists pointed out, correctly, that a transcribed region is not necessarily indicative of a biological function. They also pointed out that DNA binding proteins are EXPECTED to bind to many non-functional loci, especially in a genome full of junk DNA. A binding site does not equate to biological function... The death of junk DNA has been greatly exaggerated but it fits in nicely with a preconceived notion of mysterious dark matter and blinders that prevent you from seeing any evidence supporting junk DNA."

Claiming that 80% of the human genome serves some biological function when previous research has shown that only 2% of genome serves a biological function is quite an extraordinary claim. Changing the definition of "biological function" to support this claim seems somewhat dubious. As the old saying goes, extraordinary claims require extraordinary evidence. Judging from the mostly negative response of a the larger genetic research community it seems to me that ENCODE has failed to provide this extraordinary evidence, despite last fall's massive publication spree. Does our junk DNA do stuff? Sure, but this does not mean that the things that it does have any biological meaning.

Enter Utricularia gibba, a small aquatic carnivorous angiosperm.  U. gibba now holds the title for the smallest genome ever sequenced from a multicellular plant. Even more fascinating is that U. gibba has very little junk DNA, less than 3% - and that's using the standard definition of "biological function". That means 97% of the U. gibba genome is made up of genes (i.e. DNA that codes for proteins). This suggests that junk DNA is not a necessary for complex life.

Maybe you're wondering, "Why does U. gibba have such little junk DNA?" According to a new study published in Nature (Ibarra-Leclette et al., 2013), it would appear that U. gibba simply deletes its junk DNA because of its unique biochemistry, and not for any practical or selective purpose. I think this article on Science 2.0 summarizes this research quite nicely:

"But the scientists in this paper argue that organisms may not bulk up on genetic junk for reasons of benefit. Instead, they say, some species may simply have an inherent, mechanistic bias toward deleting a great deal of noncoding DNA while others have a built-in bias in the opposite direction — toward DNA insertion and duplication. These biases are not due to the fact that one way of behaving is more helpful than the other, but because there are two innate ways to behave and all organisms adhere to them to one degree or the other. The place that organisms occupy on this sliding scale of forces depends in part on the extent to which Darwin's natural selection pressure is able to counter or enhance these intrinsic biases."

So, does junk DNA serve an important biological function? Probably not.

Up in the trees with Australopithecus sebida

Back in February Science published a journal full of articles on Australopithecus sediba. I'm just getting around to reading it now. The first article I turned to was "The Upper Limb of Australopithecus sediba" (Churchill et al., 2013). I chose to read this article first because 1. A. sediba has the most intact upper limbs of any fossil hominin ever discovered, and 2. I just think post-cranial (and specifically upper limb) ape anatomy is fascinating.

Okay, here's the deal: some paleanthropologists think that australopithecines did not climb trees on a regular basis. Other paleoanthropologists think that australopithecines retained some arboreal characteristics long after bipedalism evolved. These days I tend to find myself in the second camp. There have been a number of recent studies which seem to indicate australopithecines retained morphological characteristics commonly found in arboreal primates. Here's a little blog post I wrote on some of that research back in January.

Last month I had the opportunity to have dinner with the legendary post-cranial anatomist and paleoanthropologist Owen Lovejoy. He's in the no tree camp. I asked him if thought australopithecines might have ever climbed trees to make sleeping nests. My argument was that it seems like a fairly logical place to avoid predators. Lovejoy pointed out that trees probably weren't a good place to hide from predators because most large cats have no problems climbing trees. Instead he suggested that australopithecines probably slept on the ground in large groups. He suggested that it was the size of these groups which would have scarred away predators. Thus, the main line of defense against night-time predators was more likely to have arisen from living in larger social groups. Good point, I hadn't really thought about that.

So, what can Churchill et al. (2013) tell us about this arboreal vs. non-arboreal debate? Well, first off it's important to point out that A. sediba really seems to show an interesting mix of primitive and derived traits. The introductory article by Lee Berger (2013) "The Mosaic Nature of Australopithecus sediba" captures this idea:

"This examination of a large number of associated, often complete and undistorted elements gives us a glimpse of a hominin species that appears to be mosaic in its anatomy and that presents a suite of functional complexes that are different from both those predicted for other australopiths and those of early Homo."

Churchill et al. (2013), however, demonstrates is that although A. sebida can generally be characterized by a mosaic of primitive and derived traits this pattern does not hold for the upper limb. The upper limb of A. sediba is extremely primitive, even more so than earlier east African australopithecines like A. afarensis and A. anamensis. I won't go into all the details as to why the upper limb is primitive - otherwise I'd just be repeating the original article (go read it yourself).

The interesting catch is that the primitive nature of A. sediba's upper limb is actually more similar to early members of the Homo genus (i.e. Homo habilis) than it is earlier east African australopithecines (i.e. A. afarensis and A. anamensis).  The last known australopithecine was more primitive than earlier forms. Weird, eh?

Well, it's not that weird if you're familiar with some of Berger's previous work. Back in 1998 McHenry and Berger wrote a paper in which they argued that A. africanus was also more similar to Homo habilis in this regard. Now, Berger (2013) is suggesting that A. sediba forms a South African clade with A. africanus which is distinct from east African australopithecines. It follows then, that the post-cranial similarities between the east African australopithecines and later members of the Homo genus are homoplasies, early members of the Homo genus arose from the South African australopithecine clade, and the eastern African australopithecine clade therefore represents an evolutionary dead end.

Simply put, A. sediba is more closely related to you than Lucy. This also suggest that those autralopithecines which are most closely related to the Homo genus were likely to have retained some arboreal characteristics rather late into their evolution, long after bipedalism evolved. I think Lovejoy still makes a good point about trees not being the safest place to sleep. So, maybe australopithecines did sleep on the ground. Maybe that was unique to east African forms. I don't know. What I do know is that trees are also full of all sorts delicious goodies like honey and birds eggs. That seems like a good enough reason to keep on climbing in my eyes.
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• Berger, L.R. 2013. The Mosaic Nature of Australopithecus Sediba. Science 230.
• Churchill, S.E., Holliday, T.W., Carlson, K.J. Jashashvili, T., Macias, M.E., Mathews, S., Sparling, T.L., Schmid, P., de Ruiter, D.J., Berger, L.R. 2013. The Upper Limb of Australopithecus sediba. Science 230.
• McHenry, H.M, Berger, L.R. 1998. Body proportions of Australopithecus afarensis and A. africanus and the origin of the genus Homo. Journal of Human Evolution 35 (1).

The comparative brain sizes of Homo floresiensis and Homo erectus

Since the initial discovery of Homo floresiensis two different hypotheses have been generated to explain its origin. One idea has is that H. floresiensis evolved from the considerably larger Homo erectus species through a well-known evolutionary process known as insular dwarfism. The suggestion is that H. erectus originally reached the area of Flores before it became an island. Once sea levels raised Flores became an island, trapping the original founder population. Overtime H. erectus decreased in size as it adapted to a new ecological niche. H. erectus fossils have been found in Indonesia predating the earliest H. floresiensis fossils, so there seems to be some evidence to support this hypothesis. Additionally, some of the other fauna from Flores, such as stegadons (an extinct elephant-like animal), seem to have undergone a similar evolutionary transition – evolving from large animals to small dwarf versions (Van Dan Bergh et al., 2008).

One argument against this idea is that the degree of difference between the cranial capacity of H. floresiensis and H. erectus is too great to be accounted for by insular dwarfism. H. erectus had an average cranial capacity of 1000 cc, whereas H. floresiensis had a cranial capacity somewhere between 380-430 cc. This has lead some researchers to suggest H. floresiensis is more likely to have evolved from a smaller hominin like Homo habilis or even an Australopithecine. Additional evidence for this hypothesis can be found in similarities between the carpal morphology of H. floresiensis and earlier, smaller, hominins (Orr et al., 2013). Essentially, H. floresiensis had a primitive wrist which does not resemble the wrist of larger, more derived late Pliocene/early Pleistocene hominins. The major problem with this idea is that no one has ever found fossil remains of H. habilis or an Australopithecine outside of Africa. As far as the fossil record tells us, H. erectus was the first hominin to disperse outside of Africa. Thus, the similarities in carpal morphology between H. floresiensis and small primitive African hominins is more likely to be a consequence of convergent or parallel evolution (homoplasy).

It should probably be noted that there some other researchers which have suggested that H. floresiensis is not a separate species, but in fact Homo sapiens suffering from microcephaly. This idea has been largely discarded, as H. floresiensis lacks a number of traits present in modern humans, perhaps the most obvious being a chin (H. sapiens and a few late-period Neanderthals are the only hominin species that have chins).

One of the problems is in sorting out these different hypothesis is that there is no consensus on the actual cranial capacity of H. floresiensis. Some reports put it as low as 380 cc whereas others have suggested a much higher capacity around 430. A new study by researchers from the University of Tokyo (Kubo et al., 2013) have sought to rectify this problem by conducting a more detailed analysis using a high resolution micro CT-scan. This has enabled them to get a much more precise and detailed measurement of the cranial capacity of H. floresiensis. Their study shows that the LB1 H. floresiensis speciemen had a cranial capacity of 426 cc.

Virtual endocast of LB1 showing reconstructed areas (Figure 2 from Kubo et al., 2013). 

On top of that Kubo et al. (2013) have also suggested that previous comparisions made to H. erectus were done using an overall species average. It is important to remember that H. erectus had a very wide geographical spread and existed for over 1.5 million years (considerably longer than our own species). As you can imagine there is a great deal of variation in H. erectus. Kubo et al. (2013) point out that if you look more closely at regional differences in H. erectus – those H. erectus populations which would have been both temporally and geographically closest to H. floresiensis were actually on the smaller than the H. erectus species average. That is to say, Indonesian H. erectus had an average cranial capacity of only 800 cc. This makes the transition from 800 cc to 426 cc a much smaller leap.

As supporters of the idea that H. floresiensis evolved from an earlier smaller African hominin are yet to discover any fossils which support their hypothesis, this new study adds a lot more weight to the idea that H. floresiensis evolved from H. erectus (albeit a regionally specific Indonesian variant of H. erectus). As an individual who is particularly fascinated with evolution in insular environments I have a certain bias when it comes to which H. floresiensis evolutionary hypothesis I tend to favor. Therefore, I’m interested to hear more ideas which contradict this new study. Anyone got any?
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Orr, C.M., Tocheri, M.W., Burnett, S.E., Awe, R.D., Saptomo, E.W., Sutikna, T., Jatmiko, Wasisto, S., Morwood, M.J., Jungers, W.L. 2013. New wrist bones of Homo floresiensis from Liang Bua (Flores, Indonesia). Journal of Human Evolution 64 (2): 109-129.

Kubo, D., Kono, R.T., Kaifu, Y. 2013. Brain size of Homo floresiensis and its evolutionary implications. Proceedings of the Royal Society B 208 (early online edition).

Van Den Bergh, G.D., Aweb, R.D., Morwoodc, M.J., Sutiknab, T., Jatmikob and Saptomo, E. W. 2008. The youngest stegodon remains in Southeast Asia from the Late Pleistocene archaeological site Liang Bua, Flores, Indonesia. Quaternary International 182(1): 16-48