Primatology.net

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.

PNAS will soon publish a paper from Mike Bruford and colleagues who isolated DNA from gorilla hair and feces and ultimately came up with a conclusion that the modern genetic composition of gorilla populations varies across different parts of their current geographic range and that this variation may be tied to Ice Age climate change and river barriers.

If that doesn’t make much sense, let me explain how such a situation would create genetic differences. During climate change between ice ages, populations that were in higher latitudes, found themselves separated physically because ice barriers formed and then collapsed, ultimately this segregated populations from one another another. Likewise, in drier climates, the tropics expanded and contracted to create isolated pockets much like what is created ice barriers. Ultimately these physical entities separated populations from one another. Also the genetic differences between gorilla populations is explained, in part, by the distance gorillas need to travel around river barriers, since in common with other large primates, they cannot cross large rivers.

Bruford comments on how this current study of gorilla population genetics is a crucial consideration,

“given the current catastrophic decline of great apes throughout Central Africa, current climate change patterns and the need to develop strategies to protect remaining populations from extinction.”

Remember when I told you that the genome of the gibbon was to be sequenced, all the way back in July of 2006? At that time, I assumed it will be finished sooner than the 3 years the NHGRI planned out for the project.

Well, I think my estimatation is right on track…. however researchers seem to have fallen into a slight speed trap.

One of the first publications has come out on this ape genome sequencing project, in the journal Genome Research. The paper is titled, “Molecular refinement of gibbon genome rearrangements,” which focuses on a interesting feature of gibbon genetics… that is also the speed trap.

See, gibbons have a genome that is rapidly evolving, more than other apes like us, gorillas, chimpanzees, etc. Parts of the gibbon genome is constantly being rearranged and broken up… which creates a problem for understanding and comparing genes between species. This genetic phenomenon is called karyotyping, and a unique arrangement is called a karyotype. If you are interested, a very prominent karyotype exists only in humans which distinguish us from other great apes.

Here’s a photo from the publishing team which,

“shows a split signal in human metaphase (chromosomes 6 and 9) and the inset image in the upper right corner shows a single signal in the gibbon genome. This is an example of a clone which spans the breakpoint of the rearrangement.”

Anyways, the whole scope of this paper is a report of these karyotypes and to open discussion on why certain karyotypes seem to evolve much more rapidly. The research also shows how Roberto et al. have developed unique ways to develop a framework in order to sequencing the entire gibbon genome, since they can’t really use a human one… due to the difference in karyotypes. Furthermore, the paper provides some insight on how evolution occurs with genomic rearrangement, as well as how chromosomes can become unstable in cancer and other genetic diseases (something I mentioned when I first anounced this project).

Here’s the abstract to the paper,

“The gibbon karyotype is known to be extensively rearranged when compared to the human and to the ancestral primate karyotype. By combining a bioinformatics (paired-end sequence analysis) approach and a molecular cytogenetics approach, we have refined the synteny block arrangement of the white-cheeked gibbon (Nomascus leucogenys, NLE) with respect to the human genome. We provide the first detailed clone framework map of the gibbon genome and refine the location of 86 evolutionary breakpoints to <1 Mb resolution. An additional 12 breakpoints, mapping primarily to centromeric and telomeric regions, were mapped to 5 Mb resolution. Our combined FISH and BES analysis indicates that we have effectively subcloned 49 of these breakpoints within NLE gibbon BAC clones, mapped to a median resolution of 79.7 kb. Interestingly, many of the intervals associated with translocations were gene-rich, including some genes associated with normal skeletal development. Comparisons of NLE breakpoints with those of other gibbon species reveal variability in the position, suggesting that chromosomal rearrangement has been a longstanding property of this particular ape lineage. Our data emphasize the synergistic effect of combining computational genomics and cytogenetics and provide a framework for ultimate sequence and assembly of the gibbon genome. ^“

The Howard Hughes Medical Institute has issued a press release with a more in depth discussion of the experimental design and results. I got the photograph from there as well as the description.

I am interested in keeping up with this research because there’s potential for an outstanding amount of information to come about from all of this. We can begin to understand how karyotyping, along with other types of genetic morphisms have been one of the selective forces in primate evolution, as well as apply this phenomenon to other aspects within science, such as medicine and cancer biology.

Today’s interesting press release from the University of St Andrews calls attention to a paper on the singing behavior of gibbons as a mechanism to ward off predators in addition to mating practices. Esther Clarke, Klaus Zuberbuhler, both of the University of St Andrews and Ulrich Reichard, of the Max Planck Institute observed the singing behavior of white-handed gibbons in Khao Yai National Park, Thailand. The experimenters said:

“We are interested in gibbon songs because, apart from human speech, these vocalizations provide a remarkable case of acoustic sophistication and versatility in primate communication. Our study has demonstrated that gibbons not only use unique songs as a response to predators, but that fellow gibbons understand them.

This work is a really good indicator that non-human primates are able to use combinations of calls given in other contexts to relay new, and in this case, potentially life-saving information to one another. This type of referential communication is commonplace in human language, but has yet to be widely demonstrated in some of our closest living relatives – the apes.

Not unlike humans, gibbons assemble a finite number of call units into more complex structures to convey different messages, and our data show that distant individuals are able to distinguish between different song types and understand what they mean. This study offers the first evidence of a functionally referential communication system in a free-ranging ape species.

Finding this ability among ape species, especially gibbons who in a sense bridge the evolutionary gap between great apes and monkeys, could shed light on when this ability developed in the primate lineage.”

Here’s the paper.

Gibbons seem to be all the rage, lately. A new biophysics paper on the gait of Gibbon bipedalism has been the most recent news that I have caught in my search of current events in primatology. The paper, “The dynamics of hylobatid bipedalism: evidence for an energy-saving mechanism?” was published four days ago in the Journal of Experimental Biology. It overviews how Gibbons moved on the ground based on the concern that there is some common energy-efficiency pattern in all primates that are fundamentally adapted to arboreal environments, but that can also stand up and walk. It turns out, they do just fine on two legs, but their gait is much different from ours.

Specifically, Evie E. Vereecke and two colleagues introduced an ‘instrumented walkway’ to the enclosure of four white-handed gibbons (Hylobates lar) in a Belgian zoo. As the apes ambled over it, their every move was filmed and every footfall recorded. The methodology reminds me of Eadweard Muybridge‘s studies on human gait.

Gibbons are anatomically much different than any other ape. They have outrageously large arms compared to their legs and rest of their bodies. This is because gibbon arm length is proportional to how the ape moves throughout its environment. The animals are much more often found swinging from limb to limb than “walking” on the ground.

Humans have two very distinct gaits, walking and running, gibbons only rarely engage in a way of locomotion that resembles our walk, where the legs are swung like pendulums. Instead, at all speeds, they propel themselves in a springy, bouncy fashion closer to our run. Here’s a video that I uploaded of a gibbon on the run.

And, unlike humans, Vereecke reports that gibbons do not use their Achilles tendons as the main spring. Vereecke hypothesizes that they might use their quadriceps muscles instead. Also unlike a human, they never have both feet off the ground at the same time. Vereecke suggests that this ‘aerial phase’ (think of this lovely expression on your next jog) should not be a requirement to call something a run.

The study concludes that gibbons make use of a energetically efficient spring-mass mechanism during bipedal locomotion.

The white-cheeked gibbon (Nomascus leucogenys) will be the next species of primate to get its genome sequenced by the National Human Genome Research Institute (NHGRI) in Bethesda, Maryland, accoridng to ScienceNOW Daily News. After decoding the human and chimpanzee sequence, the NHGRI has seen how the benefits of related genomes have helped medicine and other sciences; so the insititution has planned to sequence rhesus macaque, marmoset, orangutan, and gorilla genomes.

The work should help researchers understand primate and human evolution and the role of genes in disease, because related genomes provide a relative point of understanding what is a genetic difference between human and non-human primate and what is a genetic disease. The NHGRI plans to have the genome sequenced by three years…. but I think it will be done sooner.