Primatology.net

Primatology.net has a sister site, if you don’t know already, and that’s Anthropology.net. This evening I put up a post there that may interest any one keen to primate locomotion and/or human evolution. The post is specifically on orangutan locomotion, specifically on how some researchers have observed a set of Sumatran Orangutans exhibit bipedal tendencies.

If this sounds kinda sorta familiar to this very recent post, “On the biophysics of Sumatran orangutan swaying,” it is!  The same researchers that observed orangutans cheat the system and choose limbs that help them sway the best have published a new finding on bipedalism amongst the same population.

Before I jump into this article, I want to thank to Dave, one of our faithful visitors and commenters, who took the time to send us this Reuters news article on the current state of orangutan conservation. You should know already that orangutans are severely endangered, their populations are on the verge of genetic collapse, and the outlook for the ecosystem they inhabit is bleak.

All in all, it is a terrible situation.

Because of the logging industry and ultimately the destruction of rain forests in favor of cash crops, many orangutans have resorted to raiding palm oil plantations in Indonesia, Boreno, and Malayasia. Subsequently they are,

“branded pests for venturing out from their diminishing forest habitats into plantations where they eat young palm shoots.”

And because of this behavior, many Indonesians and Malaysians have a negative impression on orangutans. Lone Droscher-Nielsen, founder of the Nyaru Menteng Borneo Orangutan Survival (BOS) center in Central Kalimantan describes how people will,

“Kill the [orangutans] if we don’t go [to save them] … It’s cheaper to kill the orangutan than put up a fence or snare.”

Lone has photographic evidence of people that cut the hands off apes, slashed to death with machetes, and others with bullets through their foreheads.

Again, orangutans are raiding the palm oil plantations because where the plantations are now were once orangutan stomping grounds. Since their habitat is now destroyed, and food is sparce, these animals are doing what every other animal does — raid the easiest food source possible.

Palm oil is a booming industry and is considered an alternative to pricey crude oil. But it is “deforestation diesel“! It is not sustainable because the destruction wreaked on rain forests is irreversible.

I see many problems that can be remedied in this situation. The biggest and most prevalent problem here is the impression Indonesians, Borneans, and Malaysians have on the orangutan. So long as they see this great ape as a pest there will be no significant conservation impact. Public relations and education can reverse this. People need to understand they are the ones being ‘pests’ in this situation.

Secondly, with the help of the UN, who has identified the problems with habitat destruction in Indonesia, governments need to regulate rain forest with a heavy hand. The Reuters article goes on to state how the rain forests being leveled are not just homes to orangutans. Many other species are at risk, and since rain forests are dense and diverse biomes – -the conservation of them are more important than just the fate of the organgutans.

Lastly, this goes out to those of us primate conservationist who aren’t in the hot zone. We must support conservation efforts. I’m not just making a plea to send money to places like Lone’s Boreno Orangutan Survival center. That’s one way to help, another way is to send emails, post in your blogs, and help spread the word about the current state of orangutan survival. More often than not, the best conservation efforts come about from the masses who send small amounts of support than the big donors.

Related Posts:

• Rebuilding forests in an effort to save orangutans in Borneo
• Detecting Human Caused Population Collapse in Orang-utans from Genetic Data
• UN Reports that Orangutan Habitat will be gone in 15 years

In a effort to help save orangutans, Malaysian authorities are proposing a fund of 200 million ringgit (approx. 59 million US dollars) to rebuild the Ulu Segama-Malua forest in eastern Sabah state on Borneo island. The proposal covers work on 4,000 hectares of logged forests and 1,000 hectares of degraded forests (approx. total 12,355 acres).

It’s an exciting step in conservation efforts given the recent claims that orangutans could become extinct in the next 50 years without intervention.

The proposed plan is anticipated to be ready by late 2007.

A new public database has been released that overviews the status of endangered and almost extinct animals. I feel like it is a critical and timely resource, especially in regards to primate conservation efforts.

The project is called EDGE, and currently lemurs are at the top of the most critically endangered primates on that list, and sadly almost every species of lemur that I know frequent that list. Most of the animals represented on the list are small mammals, many rodents, for example. The mountain monkey of South America has made the list, and at 97 on the list of the most critically endangered is the orangutan (Pongo pygmaeus).

In other conservation news, I’m happy to report that the World Wildlife Fund has issued a statement on the rebound of mountain gorillas, in east Africa. They are,

“making a slow but steady comeback due to a decade of conservation efforts to counter the impact of war and poaching…

…There are now 340 in Uganda’s Bwindi Impenetrable Forest National Park, which is home to nearly half the world’s mountain gorillas, the global conservation group said.

That is a 12 percent growth over the past decade.”

Pretty awesome news, and I must tip my hat off to Paulin and his team, who run the blog Gorilla Protection. Let me remind you they broke the news of the two silverback males slaughtered recently. Their reports come straight from the field, and provide us with a tangible connection to the conservation effort of gorillas. If you don’t visit regularly, please do. Make sure you check out their video of a 2-day old gorilla as well as all their wonderful photos.

Last thing, Science has published some reports that came out from this year’s meeting of the American Association of Physical Anthropologists. One of the reports, related to gorillas, is a study of,

“the nuclear DNA from the two species of wild gorillas indicates that they diverged slowly into two species, apparently taking the better part of a million years.”

Since we were talking about genome comparisons this week, I thought you maybe interested in keeping track of more primate genome related science. Check out the report, here.

In almost one year of blogging here, we haven’t yet covered how the study of biophysics intersects with primatology. (Update: I realized I kinda lied, I forgot about this post on gibbon gait. Oops.)

Biophysics, in a sense, is the study of the form and function of bodies, and is formally defined as the application of the laws of physics to life processes. The ways a primate body plan is structured dictate some of the primary functions and forms of mobility. For example, humans have very robust lower-limb skeletal structures. From really dense femurs, to joints heavily padded with cartilage, our lower limbs are made to take a beating. This feature in our bodies, correlate to how we move about — bipedally.

A new study, published in Biology Letters, studies how orangutans use the sway of branches to propel themselves from tree to tree. They already have longer arms than legs, a useful adaptation to reach from branch to branch. Also their lower limbs are as flexible as our upper ones (if not more)… Isn’t that crazy?

Swaying, as their primary form of movement is way more energetically cost effective than climbing down one tree and up the next and interestingly is seen in only Sumatran orangutans. According to a Nature news report on this study,

“These are the only primates known to live exclusively in the tree canopy, in part because of the Sumatran tiger and other predators that await them on the ground.”

Pretty, interesting tangent between this form of movement and the ecological context the orangutans live in, if you ask me.

The authors of the paper used video footage of Sumatran orangutans in movement to calculate the energy orangutans use in swings, by estimating the weight, mass, and angles observed in the films and plugging them into some classical torque equations.

After all these calculations, another interesting observation was made, about orangutans selecting for ‘stronger vertical branches nearer the tree trunk,’ so that they are less likely to snap under the weight of these big guys.

If you are interested in this publication, it’s published under this title and link, “Orangutans use compliant branches to lower the energetic cost of locomotion.”

Well hot dang, I was reading Omni Brain the other day, where Steve broke the news that Atlanta Zoo’s orangutans play video games. But I didn’t post about it, not because it ain’t primatology related news, but because there wasn’t a video to support it. In my mind, if I can’t see it, it is less real. I think Steve operates in the same way because in his post he made a call to locate the video. One hasn’t surfaced yet, but I figured that since Engadget and Digg have posted about this news, its legitimate enough to follow suite.

From Australia’s The Age, “Gaming apes wow zoogoers” the basis of this behavior is explained,

“…Two Sumatran orangutans are part of new Zoo Atlanta research that uses computer games to study the cognitive skills of the primates.

The best part? Visitors to the US zoo get to watch their every computer move.

The orangutans play the games on a touch screen built into a tree-like structure in the habitat to blend in with their environment. Visitors watch from a monitor in front of the orangutan exhibit.”

The orangs actually have two games to play, one where its a matching game based on selecting,

“identical photographs or match orangutan sounds with photos of the animals. Correct answers mean food pellets.

There also is a painting game where they can draw pictures by moving their hands and other body parts around the screen. Printouts of their masterpieces are on display in the zoo.

The computer games test the animals’ memory, reasoning and learning, spitting out sheets of data for researchers at the zoo and Atlanta’s Center for Behavioral Neuroscience, a partner in the project.”

I like this project. I think it gives us an insight into how complex these great apes are. I hope it does raise awareness that orangutans are really endangered, as intended by the zoo officials. Another side benefit, is that this is a unique form of enrichment for the orangutans. Definitely not the the traditional ‘hide and go seek’ method of placing treats in puzzles, but equally as challenging.

I was thinking maybe one day we can get Kanzi, the Pacman playing chimp, to play these two orangutans? Perhaps we can have a LAN-party or something?

Towards the end of last year we posted on the anticipated release of 200 orangutans from the Nyaru Menteng Rehabilitation and Reconstruction Center in Central Kalimantan to the protected Baktikop forest. Their departure provided more room for 48 new residents from Thailand (which recently became 50 new residents).

Willie Smits (Nyaru Menteng Rehabilitation and Reconstruction Center) reports:

“Two of the orangutans have given birth, both to male babies”

It has been discovered, since their arrival at the Center, that many are dealing with tuberculosis and hepatitis. Fortunately,

“The mothers and the bab[ies] are healthy.”

Captivity does strange things to animals, but what’s happening at Taman Safari animal hospital in Java, Indonesia is outright remarkable!

They have four babies in their care who normally wouldn’t get along. From the Daily Mail article, “The deadly enemies who are the best of friends,”

“Two Sumatran tiger cubs and two baby orang-utans, each pair abandoned by their mother soon after birth, have become inseparable playmates in the nursery room…

Nia and Irma happily snuggle up to the cubs in a way that five-month-old orang-utan sisters would never normally contemplate.”

In the wild, both species are endangered and Sumatran tigers, “might normally regard a baby orang-utan as a snack.”

And now for the adorable photos:

P.S. Many thanks to Neatorama, for posting this!

A new statistical calculation called the hidden Markov model has been applied to four regions of the human, chimpanzee and gorilla genomes as reported in the PLoS Genetics journal.

But, before I jump into a discussion of the implications of this paper, let me explain to those unfamiliar with the hidden Markov model that it was,

“developed in the 1960s and originally applied to speech recognition.”

The calculation takes observable sequences, such as DNA from several genomes in this case, and seeks to fish out hidden parameters. It does this by isolating common genetic patterns from outliers throughout the genomes being compared. Of which the amount of difference and similarities can help calibrate a molecular clock. If you are curious about this statistical test, please check out Wikipedia’s entry on hidden Markov models.

In the paper, “Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model,” the authors analyze the results from these hidden Markov model calculations and claim their findings shifts the gap between human-chimpanzee divergence from 5-7 million years ago to around about 4 million years ago. Furthermore, they claim they have evidence that,

“it took only 400,000 years for humans to become a separate species from the common chimp-human ancestor.”

The abstract, if you care,

“The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human–chimp–gorilla–orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human–chimp (4.1 ± 0.4 million years), and fairly large ancestral effective population sizes (65,000 ± 30,000 for the human–chimp ancestor and 45,000 ± 10,000 for the human–chimp–gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.”

You maybe asking, how did they do this? Molecular clocks, friends, which I briefly mentioned above. Molecular clocks are effectively patterns in mutations in genomes that we expect to stay fairly consistent throughout evolutionary time. Previous molecular clocks, as reported on Time Tree, average for the time of nuclear divergence between human and chimpanzee lineages to be around 5.56 million years ago. The new hidden Markov model recalibrates, narrowing several parameters such as the time at which humans diverged from other ape lineages.

The following figures from the paper best portrary the results. You will see errors above the points plotted, and those are associated with the estimatation calculated via hiden Markov model. On the x-axis targets 1 refers to Chromosome 7, targets 106 to Chromosome 20, targets 121 to Chromosome 2, and 122 to Chromosome 20. The first is a population genetics parameter for time of divergence and the second time of speciation.

Note how a, or human chromosomes, sampled, consistently stays around 4mya.

Note how t1, or human chromosomes, compared, stays around 4mya, too. While the error bars are large, the study is pretty convincing. This study is also interesting.

It shows us that up until 4 million years ago, there was a lot of genetic introgression but a complete cessation of gene flow occurred abruptly. As John Lynch, from Stranger Fruit, points out,

“The age of 4.1 million years would apparently put the split during the time of such taxa as Australopithecus anamensis, A. afarensis and Kenyanthropus platyops. It will be interesting to see how this affects our current understanding of hominid evolution.”

Some news reports about this paper:

• Chimps, humans split only 4 million years ago
• Study moves chimp-human split to 4 million years ago

I’m gonna be sharing with you another state-of-the-orang-utan-union type article, however this time it is in the form of a scientific paper. The paper was just published in PLoS Biology, an open access academic journal… so you can read the first hand scientific accounts from anywhere. It is titled, “Genetic Signature of Anthropogenic Population Collapse in Orang-utans” and here’s the abstract (I’ve bolded what I think is the most impacting part of this paper),

“Great ape populations are undergoing a dramatic decline, which is predicted to result in their extinction in the wild from entire regions in the near future. Recent findings have particularly focused on African apes, and have implicated multiple factors contributing to this decline, such as deforestation, hunting, and disease. Less well-publicised, but equally dramatic, has been the decline in orang-utans, whose distribution is limited to parts of Sumatra and Borneo. Using the largest-ever genetic sample from wild orang-utan populations, we show strong evidence for a recent demographic collapse in North Eastern Borneo and demonstrate that this signature is independent of the mutation and demographic models used. This is the first demonstration that genetic data can detect and quantify the effect of recent, human-induced deforestation and habitat fragmentation on an endangered species. Because current demographic collapses are usually confounded by ancient events, this suggests a much more dramatic decline than demographic data alone and emphasises the need for major conservation efforts.”

The basic premise of the publication is that defrestation has impacted populations of wild orang-utans in North Eastern Borneo to such determental levels that the gene pool can’t support a viable population even if things turn for the better. That was a bit hard for the authors to prove because the effects of very recent human caused population fragmentation among orang-utans on genetic diversity are typically difficult to demonstrate. How can one attribute human caused population fragmentation as the sole factor? What if other things are going on?

In order to answer that question and factor out any other variables the authors first limited their study to orang-utan populations in the,

“Lower Kinabatangan floodplain in Eastern Sabah, a region that has experienced large-scale commercial timber exploitation and agriculture since the mid-1950s. Faecal and hair samples were collected from wild orang-utans during boat surveys along the Kinabatangan River or during line transects to estimate nest densities. Two hundred different animals were genetically identified using 14 microsatellites.”

So they have a pretty large sample size from a region where there’s been a long standing history of human impacted ecological change. That makes for a pretty strong foundation upon to make conclusions. Next, they basically ran three different but complementary tests in order to detect, quantify, and date the decline in orang-utan populations. Here’s a two part summary of the three tests:

1. “The first approach is based on summaries of the allelic frequency spectrum and was used to detect either a population expansion or decline. It relies on the loss or excess of rare alleles expected in bottlenecked or expanding populations, respectively, and uses simulations under different mutation models to detect departures from mutation-drift equilibrium.”
2. “The two other approaches used were Bayesian methods using the information from the full allelic distributions and shall be referred to as the Beaumont and the Storz and Beaumont method… The two Bayesian methods were applied to two subsets of the data for computational reasons.”

From these tests the authors concluded the following results. The first test yielded an observation that, “all nine samples exhibit a strong and significant signal for a population bottleneck, through the loss of rare alleles.” That just means orang-utans are losing their diversity. There’s no definitive conclusion on what that will do, and when that will cause the orang-utan population to collapse… but it is pretty indicative that once you lose diversity, the probability of survival amongst your population reduces. The second test confirmed the conclusion from the first test or in their words, “the present-day genetic structure of orang-utans is strongly influenced by a dramatic decrease in population size, with no support for growing or even stable populations.” And the last test quanitified a date upon which the population of orang-utans will collapse due to a lack of genetic diversity… and that will be on or before 210 years from now.

That’s such a low blow. I don’t know which is worse news, that orang-utan habitats will be erased within 15 years if we continue deforestation at the rates they are going on at or that this is all futile and orang-utans are so endangered that there’s no hope for them a couple centuries down the line. Now there’s a possibility that the computer models, algorithms, and statistical analysis the authors of this paper used are just probabilities… but it does seem that either way orangs-utans are screwed.

In the last century or so, we have killed off 95% of orang-utans. That statistic by itself is crazy. They are a unique and vital species of great ape. They are the only other great ape, other than humans, who live outside of Africa, and deserve our best efforts for conservation. The first thing we must do, as I advocated earlier, is to cut our dependance on illegal logging. That is something we can all do personally. Use less fresh paper, recyle and reuse. The next thing that needs to be done is to step up efforts in creating a diverse genetic population of orang-utans in captivity. That’s all we got. I hope zoological insitutions step up to the plate and devise a plan to accomplish this common goal…