Primatology.net

It seems like the news hasn’t gobbled up this news as adamantly as it did the news of the bonobo reserve in the Congo, but it is nonetheless newsworthy and crucial to the study of bonobos. The Department of Evolutionary Anthropology at the Max Planck Institute put out a press release that they just acquired a second Genome Sequencer FLX (GS FLX) System from 454. Svante Pääbo, director of the department, plans to put this one to use in sequencing the bonobo genome.

I’ve seen two of these 454 devices in person, over at the JGI. These things are gnarly, and cost a lot of money. I was told that each time you wanna use one of the machines, the reagents alone cost thousands of dollars. I didn’t ask to see a purchase order or anything, but I believe them. These devices do big science, they sequence small fragments of DNA and help on constructing it and they do it well.

You maybe asking, “What good does a bonobo genome do for us? We got chimpanzee, macaque, human… and we’re getting Neandertal, gorilla, and gibbon!” Well exactly that, the more primate genomes we have the more information we can get when we compare the genomes to one another. For example, between the bonobo, chimp, Neandertal, and human genomes we can screen to see what genes are specific to modern humans and what genes are specific to chimpanzees. This is critical in understanding what makes us all different, since it is proposed we share so much together.

In related news, I’m happy to announce that the Sankuru Nature Reserve a 11,803 square miles will be created through a partnership involving American and Congolese conservation groups and government agencies to help preserve bonobos. Lots of press has covered this news, for example here’s the New York Times coverage. As you may know all great apes are severly threatened if not endangered.

The collective understanding of Miocene African primate evolution, especially ape evolution, is generally unfounded. Why? Because the fossil record is spotty, there are only a handful of primates from the Miocene. The Miocene lasted from 23.8 to 5.3 million years ago, and a lot of interesting things happened in the ape lineage during that time. The molecular evidence tells us that gorillas diverged about 10 to 8 million years ago, and chimpanzees as early as 5 million years ago. But because we don’t have many fossils from that period, it’s hard to see what these apes looked like during this period.

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.

I could swear that in the past I had covered news that the minute genetic and massive phenotypic differences between humans and chimpanzees are due to the alternative splicing. But I can’t seem to find the post at all… there maybe a slight chance I didn’t post about it but I’m pretty sure I did cause this is the kind of science that I love to gobble up. Oh well… I guess it all doesn’t really matter because University of Toronto researchers, Benjamin Blencowe and John Calarco, have discovered significant differences in the way genetic material of humans and chimpanzees are spliced to create proteins.

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.

In August, 2007 Gen Suwa and crew reported on a new Ethiopian Miocene Ape, Chororapithecus abyssinicus. And today, Kenyan and Japanese paleoanthropologists have published their study of a fragment of a mandible and 11 teeth, dating back to between 9.8 and 9.88 million years, which was found 2005.

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.

I’ve been meaning to post about this interesting find for almost two weeks now, but I haven’t gotten around to it until now. What you see is a very impressive statue of a gorilla made out of coat hangers. The artist that I tip my hat to is David Mach.

I’ve been unable to post on a lot of important primatology news as of late, I’ll try to catch up this weekend.

But I’m making time to quickly announce that Washoe has died. She was 42 years old and one of the first apes that was taught sign language, about 300 signs. She was known for her sweet, endearing soul. She even made signs for words she didn’t know.

Rest in peace, Washoe.