Primatology.net

Last October, London Zoo saw the birth of a new baby gorilla? He has since been named Tiny and he’s walking now.

London Zoo's Tiny

The orangutan genome has been sequenced and published in today’s Nature. The paper, “Comparative and demographic analysis of orang-utan genomes,” is open access for you to read for yourself. I’ll be highlighting some of the high points in this post. Devin Locke, a structural geneticist at Washington University School of Medicine in St. Louis, Missouri, headed the sequencing of six Sumatran and five Bornean orangutans. As you may know Pongo abelii, or the Sumatran orangutan, is a separate species from Bornean orangutans — Pongo pygmaeus.

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

Kristin Abit is a new guest blogger here at Primatology.net. She is currently a Master’s student, studying Sustainable Development and Conservation Biology at the University of Maryland. Her undergraduate degree was in Biology and Psychology from Loyola University, also in Maryland.

Kristin has over 5 years of experience in the zoo field as an animal keeper. She primarily cared for lemurs and Old World monkeys. She also participated in field research experiences in Costa Rica and Malaysian Borneo. Her research interests focus on improving animal wellbeing through applied research in the captive setting, especially relating to environmental enrichment and animal management. In a border scope, she also tells me she is interested in conservation education and conservation psychology.

I left primate care several years ago, so I’m happy to have someone like Kristin, with so much primate care under her belt, help us out. I’m looking forward to reading her posts!

It is with great pleasure to introduce a new member to our Primatology.net blogging family, my good friend Allison Hanes. We both attended UCSC for our undergraduate degrees and became friends while taking some prerequisite courses. Allison got her Bachelor of Arts degree in Environmental Studies/Biology. She’s enrolled as an MSc student in the Primate Conservation program at Oxford Brookes University.

She has worked over five years as a veterinary technician, has had research experience with the Shusterman Pinniped Group at UCSC Long Marine Laboratory, and has an extensive wildlife-related volunteering record. Her interests include veterinary medicine, ecotourism, community-based conservation, sustainable development, and conservation medicine.

She’ll be publishing a post here in the near future, so make sure to keep an eye out. Again, she’s been my friend for over 10 years and I’m very enthusiastic about having Allison on board. I believe she’ll offer a great mix of topics and look forward to reading her posts.

This image puts a whole new perspective to the Nintendo classic game, Donkey Kong. At the San Fransisco Zoo, a boy dropped his Nintendo DS into the gorilla enclosure. The following happened. I’m particularly loving the little one’s expression and body language.

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

Plasmodium falciparum infecting Red Blood Cells

Plasmodium falciparum is the protozoan parasite that causes malaria in humans and ultimately the death of 2-3 million people a year. If you didn’t know, malaria is one of the most common infectious diseases and an enormous public health problem. Only one other malaria causing protozoan, a sister species of the P. falciparum parasite, P. reichenowi, was known to cause malaria but infects only chimpanzees. That was until researchers based in Gabon and France began sampling pet chimpanzees.

The team collected blood from 19 wild-borne animals kept as pets by villagers in Gabon, 17 of them being chimps. They found out that infected by a Plasmodium parasite, but sequencing of the parasite’s whole mitochondrial genome showed that it wasn’t P. falciparum nor P. reichenowi. Rather, it was a new species more closely related to P. falciparum. They classified the new species as P. gaboni.

Phylogenetic relationships among Plasmodium species (including P. sp_K) and associated host groups.

They have published their findings in the open access journal PLoS Genetics, under the title, “A New Malaria Agent in African Hominids.” You maybe asking why this is relevant to primatology? Many are against studies that use primates like chimpanzees because of ethical reasons. In situations like this, chimpanzees already infected with the parasite are useful to sample and study to shed light on the genomic adaptations of P. falciparum to humans and thus help in the discovery of new potential drug targets.

Ollomo, B., Durand, P., Prugnolle, F., Douzery, E., Arnathau, C., Nkoghe, D., Leroy, E., & Renaud, F. (2009). A New Malaria Agent in African Hominids PLoS Pathogens, 5 (5) DOI: 10.1371/journal.ppat.1000446

As you may have noticed, it has been rather silent here for the last 5 months. I’m happy to break the silence with most excellent news of a new guest blogger to Anthropology.net & Primatology.net, Raymond Ho, of The Prancing Papio. I’ve been an avid reader of Raymond’s blog ever since he started it earlier this year. His balance in being thorough, inquisitive, and consistent has kept me subscribed.

For a little background on Raymond, he’s currently an undergraduate Biological Anthropology student at CUNY, Queens College and is expected to graduate next month. As you can tell from the title of his personal blog, he’s passionate about primatology, especially grooming. His senior honors thesis compares grooming between hamadryas baboons and gelada baboons. But he does write on many anthropological topics as well, such as paleoanthropology — one of my favorite topics!

I’d like to extend a warm welcome to Raymond for accepting to blog here. I’m very grateful, actually, especially since I’m still an inactive member of this site and hope that he and others will keep this site ticking in my absence. If you haven’t followed his blog, I suggest you do. He’ll continue posting there and here.