One remarkable finding of the study is the estimated divergence between the Sumatran and Bornean species. The team calculated the two species diverged 400,000 years ago. We know that land bridge between Indonesia’s Sumatra and Borneo split at least 21,000 years ago but until now we’ve never known at what time the two speciated.

Compared to the two other great apes whose genomes have been sequenced, humans and chimps, the orangutan genome has changed much less. We’re still waiting on the gorilla genome to be finished. Oangutans originated some 12 million to 16 million years ago. Theoretically, orangutans have had more time to accumulate  genetic variation compared to humans and chimpanzees, which split into their own lineages 5 million to 6 million years ago. One would expect at least twice as much variation in the orangutan genome. However, in the study, a comparison of the three genomes shows that humans and chimpanzees have lost or gained new genes at twice the rate of orangutans.

Why’s that?

The paper explains that orangutan genomes have much fewer active retrotransposons than human and chimp genomes. Retrotransposons, or Alu elements, are essentially jumping genes, that replicate, and amplify then insert into different parts of the genome. The initial 2001 draft of the human genome reported that around 42% of the human genome is made up of retrotransposons. The authors of the orangutan paper illustrate that the human genome has ~5,000 Alu elements, whereas the orangutan genome has 250. This is significantly different. The authors write,

“Reduced Alu retroposition potentially limited the effect of a wide variety of repeat-driven mutational mechanisms in the orang-utan lineage that played a major role in restructuring other primate genomes.”

Personally, and this is my thinking here nothing the authors say — a common source of many human retrotransposons are to prehistoric viruses that integrated into our ancestral DNA. Viruses are communicable. Orangutans are the most solitary Great apes. I suspect they would have much less exposure to viruses because of their social structure, and thus much less chance of insertion of retrotransposon. Again, this is a hypothesis of mine, and I could be very wrong to think this.

Comparison of Orangutan to Great Ape Alu sequences

One last finding, I want to bring up was published in another paper released by the same team, but in the journal Genome Research. In the paper, “Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection,” coauthors of the previous study write that there are many similarities to the human and orangutan genome, much more similar than human to chimp, in fact. They suspect that could be because humans split from a common ancestor with chimps, of which both species had the same ancestral orangutan DNA. What remains curious is that humans and chimpanzees have evolved separately for millions of years. In the process, chimps for mysterious reasons lost some orangutan DNA that humans retained.

As often in sciences, many more questions arise from studies like these but I am excited that the age of genomics is shedding more light on our fellow primates!

Locke, D., Hillier, L., Warren, W., Worley, K., Nazareth, L., Muzny, D., Yang, S., Wang, Z., Chinwalla, A., Minx, P., Mitreva, M., Cook, L., Delehaunty, K., Fronick, C., Schmidt, H., Fulton, L., Fulton, R., Nelson, J., Magrini, V., Pohl, C., Graves, T., Markovic, C., Cree, A., Dinh, H., Hume, J., Kovar, C., Fowler, G., Lunter, G., Meader, S., Heger, A., Ponting, C., Marques-Bonet, T., Alkan, C., Chen, L., Cheng, Z., Kidd, J., Eichler, E., White, S., Searle, S., Vilella, A., Chen, Y., Flicek, P., Ma, J., Raney, B., Suh, B., Burhans, R., Herrero, J., Haussler, D., Faria, R., Fernando, O., Darré, F., Farré, D., Gazave, E., Oliva, M., Navarro, A., Roberto, R., Capozzi, O., Archidiacono, N., Valle, G., Purgato, S., Rocchi, M., Konkel, M., Walker, J., Ullmer, B., Batzer, M., Smit, A., Hubley, R., Casola, C., Schrider, D., Hahn, M., Quesada, V., Puente, X., Ordoñez, G., López-Otín, C., Vinar, T., Brejova, B., Ratan, A., Harris, R., Miller, W., Kosiol, C., Lawson, H., Taliwal, V., Martins, A., Siepel, A., RoyChoudhury, A., Ma, X., Degenhardt, J., Bustamante, C., Gutenkunst, R., Mailund, T., Dutheil, J., Hobolth, A., Schierup, M., Ryder, O., Yoshinaga, Y., de Jong, P., Weinstock, G., Rogers, J., Mardis, E., Gibbs, R., & Wilson, R. (2011). Comparative and demographic analysis of orang-utan genomes Nature, 469 (7331), 529-533 DOI: 10.1038/nature09687

Hobolth, A., Dutheil, J., Hawks, J., Schierup, M., & Mailund, T. (2011). Incomplete lineage sorting patterns among human, chimpanzee and orangutan suggest recent orangutan speciation and widespread selection Genome Research DOI: 10.1101/gr.114751.110

Els Hostalets de Pierola, Barcelona, Catalonia, Spain

By way of Afarensis is news of a new Middle Miocene hominoid species found from the Abocador de Can Mata site in Spain. It is classified as a great ape with many afropithecid and several kenyapithecine features which I’ll give an overview of in a bit. Furthermore, the specimen, IPS43000, is 11.9 million years old, dated via magnetostratigraphic series and associated fauna from the strata it was recovered in.

The authors have published the paper in the journal PNAS under the title, “A unique Middle Miocene European hominoid and the origins of the great ape and human clade.”

What’s unique about this hominoid, aptly named Lluc or enlightenment in Latin, is that it has a very modern face… In other words it’s got a reduced facial prognathism. The specimen includes a fragmented cranium that with most of the face preserved and the associated mandible. While the muzzle of Lluc is so reduced that only find comparable values within the genus Homo, Lluc’s got an array of primitive features, such as super thick dental enamel and teeth with bulbar cusps. The mandible is also very robust. All of which are characteristics of afropithecids — primitive hominoids from the African Middle Miocene.

Anoiapithecus brevirostris (IPS43000)

But other more derived features, like the forward positioning of the zygomatic bone and a bold mandibular torus along with a a reduction in the maxillary sinus, are shared only with the kenyapithecines. Kenyapithecines are a group of apes that ever dispersed outside the African continent and colonized the Mediterranean region, by about 15 million years ago, and are collectively grouped in the genera Kenyapithecus and Griphopithecus.

Ultimately, you can see how this specimen (IPS43000), Anoiapithecus brevirostris, has a combined a set of features that until now had never been found from the fossil record. The array of features allows us enables to identify two possibilities to be the ancestral form to our family (Kenyapithecus and Griphopithecus). The authors take a leap of faith here arguing that when one takes into account that these two genera cannot be considered members of the family Hominidae yet, because they lack its basic diagnostic features, they find it obvious that the origin of our family is a phenomenon that took place on the Mediterranean region during the time span comprised between their arrival from Africa by about 15 Ma, and about 13 Ma, when we began to find in els Hostalets the first members of our family.

Moya-Sola, S., Alba, D., Almecija, S., Casanovas-Vilar, I., Kohler, M., De Esteban-Trivigno, S., Robles, J., Galindo, J., & Fortuny, J. (2009). A unique Middle Miocene European hominoid and the origins of the great ape and human clade Proceedings of the National Academy of Sciences DOI: 10.1073/pnas.0811730106

The published their results in the American Museum of Natural History’s journal, Novitates. The title of the paper is, “Estimating body mass in New World “monkeys” (Platyrrhini, Primates), with a consideration of the Miocene platyrrhine, Chilecebus carrascoensis,” and it is open access. Flynn and colleagues made 80 measurements from the skulls, jaws, and teeth of 17 different species of living New World monkeys that ranged across the full spectrum of body sizes and calculated the encephalization quotients (E.Q.’s) — the ratio of brain size relative to their body size.

They took this matrix of E.Q.’s and applied it on the skull of a primitive primate dating to 20 million years ago, the early platyrrhine Chilecebus carrascoensis. Chilecebus is the oldest and most complete well-dated primate skull from the New World. It was described by Flynn and collaborators in 1995 in this Nature paper, “An Early Miocene anthropoid skull from the Chilean Andes.” Their results of the new paper showed that Chilecebus weighed around 583 grams and had an E.Q. ratio of only 1.11—a much smaller relative brain size than any living New or Old World anthropoid, which have E.Q.’s ranging from 1.39-2.44. This suggests that the larger brain sizes seen in both groups today evolved independently.

Sears, K.E., Finarelli, J.A., Flynn, J.J., Wyss, A.R. (2008). Estimating body mass in New World “monkeys” (Platyrrhini, Primates), with a consideration of the Miocene platyrrhine, Chilecebus carrascoensis. Novitates, 3617, 1-32.

Flynn, J.J., Wyss, A.R., Charrier, R., Swisher, C.C. (1995). An Early Miocene anthropoid skull from the Chilean Andes. Nature, 373(6515), 603-607. DOI: 10.1038/373603a0

The scope of this paper is a report on tool use seen in a male chimpanzee from Guinea. Tool use has been documented in several other wild chimpanzee societies, most notably was Goodall’s observations of Gombe chimps using tools. Since then other researchers have seen other wild chimps use tools, particularly using rocks to crack nuts open, and using twigs and sticks to fish or dip for ants. Ever so recently, we read and saw a Fongoli chimp hunt with a makeshift spear.

The clincher behind chimpanzee tool use in the wild use has been that it seems to be localized within the group that the behavior is observed in. This has gotten many researchers to hypothesize that this is some group specific behavior, a cultural trait per say. Researchers had no idea how tool use behaviors emerged in these respective groups, nor how long they have been practicing tool use.

In this new study, JJ, the male chimpanzee was the only chimpanzee in his group seen selecting for sticks used to fish for ants in a two year time period. This group of chimpanzees from Bossou has been studying for 27 years and this behavior has never been observed before. So his tool use tendencies seem to be novel amongst this group. Throughout the two years of observation, JJ progressively modified the optimal fishing stick, selecting for shorter and shorter ones. This indicates that JJ learned the characteristics of the best tool, one that would yield more ants.

Unfortunately, no observation has been made of JJ transmitting this behavior to other Bossou chimps. But it does indicate several thing… tool use can independently arise in chimpanzees, regardless of the fact that the group as a whole practices tool use or not. Also, it provides an insights into the cognitive capacity of wild chimps, like JJ, to problem solve and modify their behavior.

Yamamoto, S., Yamakoshi, G., Humle, T., Matsuzawa, T. (2008). Invention and modification of a new tool use behavior: ant-fishing in trees by a wild chimpanzee (Pan troglodytes verus) at Bossou, Guinea. American Journal of Primatology DOI: 10.1002/ajp.20544

Specifically the orangutans were using sticks to pry open pulpy fruits that have “Plexiglas needles” capable of delivering a painful jab covering them. Using the tools, the orangutans were getting past handling the prickly husk and into the nutritious fruit. From an anthropological viewpoint, tool use represents an aspect of culture, since the entire group participates in a behavior that has developed over time. One unique thing to clarify is that only Sumatran orangutans have been observed to use tools, not orangutans from Borneo.

Recently, Gerd Schuster co-author of Thinkers of the Jungle: The Orangutan Report, took this photograph of,

“a male orangutan, clinging precariously to overhanging branches, flails the water with a pole, trying desperately to spear a passing fish…

The extraordinary image, a world exclusive, was taken in Borneo on the island of Kaja…

This individual had seen locals fishing with spears on the Gohong River.

Although the method required too much skill for him to master, he was later able to improvise by using the pole to catch fish already trapped in the locals’ fishing lines.”

Pretty awesome image, no? If you wanna read more about orangutan tool use, here are three papers on the topic:

Schaik, C.P., Fox, E.A., Sitompul, A.F. (1996). Manufacture and use of tools in wild Sumatran orangutans. Naturwissenschaften, 83(4), 186-188. DOI: 10.1007/BF01143062

Call, J., Tomasello, M. (1994). The social learning of tool use by orangutans (Pongo pygmaeus). Human Evolution, 9(4), 297-313. DOI: 10.1007/BF02435516

van Schaik, C.P. (2003). Orangutan Cultures and the Evolution of Material Culture. Science, 299(5603), 102-105. DOI: 10.1126/science.1078004

Suffice to say, it is always welcoming to read of a new publication announcing a new Miocene ape. We’ve had the pleasure to do so, with the introduction of Nakalipithecus nakayamai, a Miocene Ape from Kenya. PNAS is carrying the paper now, under the title, “A new Late Miocene great ape from Kenya and its implications for the origins of African great apes and humans.” The paper is written by both Japanese and Kenyan academics.The fossils of N. nakayamai were found over a decade ago in a fossil bed called Nakali, which is about 40 kilometers west of Maralal. These fossils make up the holotype of the species, which is the scientific way of saying this is the type specimen. A total of 11 fossils make up this specimen, including a right mandibular fragment with M1–M3, left I1, right C*, right P3, left P4, right M1, right I2, left P3, right P4, right M, left M, and a left dp.

As you can see, these are all teeth. Teeth are especially important in understanding evolution because they offer more resolution of information than other parts of the skeleton.

The teeth are similar in size to modern orangutans and gorillas, some of the larger great apes. The teeth differ from other known species of apes in having a much different upper canine. I’m not gonna rehash how it’s different because it requires an intimate understanding of tooth anatomy, morphology, and terminology. Just take my word for it, it’s a much different canine, as long as it is broad. Have a look for yourself,

The premolars are also different. They are elongated but have reduced cusps.The authors indicate that N. nakayamai is similar to another genus of Miocene ape, Ouranopithecus. However, the differences from Ouranopithecus are in thinner enamel and less inflated cusps in the molars. The authors compare the fossils to other Miocene apes,

“N. nakayamai is distinguished from Ankarapithecus, Sivapithecus, and Khoratpithecus by its large size… more gracile mandibular body… N. nakayamai is [also] different from Dryopithecus in its large size.”

Other than Samburupithecus kiptalami, there aren’t many mid-Miocene apes from Africa known at this time. There is a relatively larger number of Miocene ape fossils found from Turkey and Greece, which has gotten a lot of people, ahem David Begun, to think that apes made a rendezvous out of Africa and into what is now the Middle East and parts of Europe. With this new genus and species, Nakalipithecus, we now see that at least three diverse species of non-cercopithecoid catarrhines survived through the Middle to Late Miocene in Africa, and that suggests a less likelihood that hominoid primates were absent from Africa and were reintroduced from Eurasian populations.

Here’s a very brief introduction into splicing… Splicing is a type of modification of a gene that happens after a sequence is transcribed. What actually happens is that introns of pre-messenger RNA (pre-mRNA) are removed and exons of it are joined. I remember exons as expressed sequences and introns as intervening sequences.

This process produces the mature messenger RNA (mRNA), which then undergoes translation and ultimately becomes a protein. In many cases, the splicing process can create a range of unique proteins by varying the exon composition of the same messenger RNA. This phenomenon is then called alternative splicing. The illustration to your right documents what’s happening.

Blencowe comments,

“It’s clear that humans are very different from chimpanzees on several levels, but we wanted to find out if it could be the splicing process that accounts for some of these fundamental differences. The surprising thing we found was that six to eight per cent of the alternative splicing events we looked at were showing differences, which is quite significant. And those genes that showed differences in splicing are associated with a range of important processes, including susceptibility to certain diseases.”

He and his team have published their findings in the Journal of Genes and Development. The paper, “Global analysis of alternative splicing differences between humans and chimpanzees” can be summarized in one sentences, alternative splicing process differs significantly between humans and chimpanzees and is one of the main reasons as to why humans and chimpanzees are so different phenotypically but so similar genetically.

The fossils were unearthed in volcanic mud flow deposits in the northern Nakali region of Kenya. It has been dutifully dubbed Nakalipithecus nakayamai, the genus assigned after the area it was found in while the species is named after Japanese geologist Katsuhiro Nakayama who died while working on the project. Comparisons of the size of the teeth of N. nakayamai shows that it was comparable to a modern female gorilla and a female orangutan. It also resembles another Miocene ape Ouranopithecus macedoniensis, from Greece but several aspects of the dentition indicate a less specialized diet than Ouranopithecus, and place Nakalipithecus in a genus of its own.

I’ll report more on this when I get my hands on the paper.

“traits that [chimpanzees and humans] share, like altruism and vengeance, and those we don’t, like spite and most social learning skills, are shedding light on what it means to be human.”

So check out the article, “Animal Insight.” It is a pretty good review.

“The bonobos at Lola use tools. It’s really amazing because no one’s seen tool use in bonobos in the wild before (I don’t think).And everyone’s always going on about chimps using tools and how it’s so amazing because everyone used to think that’s what makes us human, and now bonobos use tools too.

Tool using is important because we think that’s how early humans got their start. We couldn’t run fast like a cheetah, and we weren’t strong like mammoths, so we started using tools like spears to hunt meat and rocks to open nuts. These days we use tools like crazy. In fact, we can’t do anything without tools. But looking at chimps, and now the Lola bonobos, we can catch a glimpse of how it all started.”

Jump on over to the post to see the video of one of the bonobos using a rock to hammer open some nuts.