orangutans

The Telegraph has a Roger Highfield article about those zany Neanderthals.

I can't get over the reconstruction that accompanies the article:

Picture from article in the Telegraph, with caption: A model head of Neanderthal man created by Maurice Wilson of the Natural History Museum, London

Those eyes say something to me, something very familiar....

(via Gene Expression)

In a less recognized article in Current Biology, Fischer et al. (2006) report on the genetic diversity of ape subspecies.

Here's the meaty part of the abstract:

Finally, we find that the extent of genetic differentiation among "subspecies" of chimpanzees and orangutans is comparable to that seen among human populations, calling the validity of the "subspecies" concept in apes into question.

Previous studies of ape population structure have mostly been based on one locus (mtDNA), with a few using the Y chromosome and nuclear microsatellites. This study adds nuclear sequences to the mix, from 16 to 26 loci. The multiple-locus perspective is important, because demographic structure can be tested only through its similar effects on different unlinked loci. The use of sequence adds a time depth that may not be as evident from microsatellites, since they have markedly faster mutation rates. For instance:

The two orangutan populations have a significantly positive Tajima's D, because of an excess of intermediate frequency alleles, which is best explained by a recent reduction in population size or by population subdivision. Using 14 microsatellites, Goossens et al. [3] showed that the excess of intermediate allele frequencies in an orangutan population from Borneo can be explained by a very recent decline in population size, mainly as a result of human activity. Because it would take much more time to be able to detect this effect in nuclear DNA, and because our orangutan samples come from different local groups (see Table S1), population structure is a more likely explanation of our observation (Fischer et al. 2006:1134).

Despite the conclusion and abstract, there is not too much different in this study compared to previous work. For instance, the F_ST estimated between orangutan subspecies is 0.28, which is at least double that estimated between human races for the same loci. Similarly, the F_ST between Eastern and Western chimpanzees (Pan troglodytes schweinfurthii and P. t. verus) is 0.32. These estimates show a considerably higher degree of population structure in these ape species compared to humans. The F_ST between orangutan subspecies doesn't represent quite the high division between these two groups, because of the extensive sequence variation within each of the subspecies.

One difference is surprisingly slight: the F_ST between central and eastern chimpanzees is only 0.09. This is the same as estimated between Chinese and Italians in the study, placing chimpanzee subspecies differences inside the range of human racial differences.

Or does it? The study also obtains the average pairwise difference between these populations, finding that the average difference between central and eastern chimpanzees (0.20 percent) is about the same as that between central and western (0.21) and eastern and western populations (0.20). Now, again as for the orangutans, the average pairwise difference among chimpanzee populations is inflated by the relatively great diversity within chimpanzee populations -- but not so much. F_ST is a measure of how many variants are shared by two populations (formally, it measures a reduction in heterozygosity attributable to population structure). So the results tend to indicate that eastern and central chimpanzees share a lot of alleles, amid a relatively high amount of diversity.

Why should that be? One explanation is a recent colonization of the eastern range (or more narrowly, the part represented by their sample of reserve chimpanzees from Kenya) by chimpanzees of central African origin. A widespread recent colonization might also explain the evidence of mtDNA disequilibrium in eastern chimpanzees.

Or, the low F_ST could represent a history of gene flow between central and eastern African chimpanzees. Fischer et al. apply a mixture of these explanations, which they also apply to the orangutans:

With respect to the duration of physical separation, the Dahomey gap that separates western and central chimpanzees was covered with rainforest until about five thousand years ago, and Sumatra and Borneo were physically connected until ten to twenty thousand years ago. Thus, the time of separation of the "subspecies" by geographical barriers has certainly been too short for complete lineage sorting by genetic drift and shorter than the separation of many human groups. In addition, migration between the groups may have occurred subsequent to the emergence of these geographical barriers. Indeed, we speculate that a more geographically complete sampling of chimpanzees and orangutans with noninvasive samples from the wild as well as samples from museum specimens in areas where apes are now extinct will eventually demonstrate that the overall picture of genetic variation within chimpanzees and orangutans is one of isolation by distance, as is largely the case among humans (Fischer et al. 2006:1135, citations omitted).

Naturally, both factors are important -- the initial movements of these apes to their current locations, sometime during the Pleistocene, and the subsequent movements of individuals between populations. The question of gene flow is important because it delimits the extent to which adaptive variants can spread from their point of origination -- and thereby circumscribes the degree to which all chimpanzees today may be different from their common ancestors. In other words, gene flow would allow multiregional evolution of these ape species over time.

But there's no real reason to say that these weren't subspecies. They were genetically differentiated after their initial origin and retained substantial genetic distinctions between them over time. "Subspecies" is a nebulous category, but it is generally defined as an evolutionary lineage within a species, which these populations would appear to be. They're not species, after all.

The only real question is what the spatial differentiation of these populations looks like -- are there long clines of genetic variation within chimpanzees as there are within human populations? For that, we will have to sample many more chimpanzees. For orangutans, the answer today is presumably "no", because the subspecies are on islands, and themselves are highly fragmented into small populations.

References:

Fischer A, Pollack J, Thalmann O, Nickel B, Pääbo S. 2006. Demographic history and genetic differentiation in apes. Curr Biol 16:1133-1138. DOI link

I'm reading a new paper by Benoit Goossens and colleagues (2006) in PLoS Biology, called "Genetic signature of anthropogenic population collapse in orang-utans". The abstract:

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.

Basically, the claims are that genetic variation shows that orangutans on Borneo began crashing in population size within the past century or so, and that disputed census figures from the 1980's that estimated a very large population of orangutans (then) may have been accurate, since the ongoing collapse has been very rapid.

I have to say, I'm not sure about this one. There's quite a bit of "fighting with the method" in this paper which to me is never a good sign. The main analysis is a Boolean method, and they emphasize repeatedly how conservative their prior assumptions are. They could be right, but that's not really the problem.

The biggest potential problem is population structure, which previous studies (e.g., Warren et al. 2001) suggested was very strong among Bornean orangutans. This study notes that population structure within the population that they sampled is relatively slight, with low F_ST between groups. Of course, that doesn't quite answer the question, since the analysis of demographic structure depends on a paucity of young rare alleles and an excess of old intermediate-frequency ones. Since populations on Borneo haven't necessarily been historically isolated, these old alleles might easily come from other Bornean populations, the ones that according to Warren et al. (2001) have a mean genetic divergence over 800,000 years ago.

So I'm not so sure about the demographic interpretations here. Hard to say that the problem of population structure would result in the signature of very recent collapse (instead of, say, a more ancient event), but collapses are tricky to interpret -- expansions are much more straightforward.

In this case, there is no chance that genetics are picking up a population crash that has been going on since the 1980's -- that is so recent that there should be barely any new rare alleles to miss in a sample. The idea that a collapse since 1980 is supported by a collapse ongoing since 1900 is pretty tenuous. The paper's best claim is that population collapse didn't start a long time ago -- say when humans first reached Borneo, for example. Their analyses certainly support that point -- orangutans may have coexisted with humans well enough as long as people weren't cutting down the forest. But I'm not sure that the analyses aren't affected by population structure in a way that would mess up these estimates.

References:

Goossens B, Chikhi L, Ancrenaz M, Lackman-Ancrenaz I, Andau P, Bruford MW. 2006. Genetic signature of anthropogenic population collapse in orang-utans. PLoS Biol 4:e25. Full text

Warren KS et al. 2001. Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus. Mol Biol Evol 10:472-480.

Nice interview touching on Carel van Schaik's new book, Among Orangutans : Red Apes and the Rise of Human Culture. Much on van Schaik's observations of orangutan sociality in densely occupied forest, including tool use (via Gene Expression).

An excerpt:

Q. What were you looking for in the Suaq swamp?

A. We'd been working in a mountainous area in northern Sumatra, and it felt as if we were missing the full picture of orangutan social organization. All higher primates - all of them - live in distinct social units except for the orangutan. That's a strong anomaly, and I wanted to solve it.

Q. How was Suaq different from other orangutan habitats?

A. It was an extraordinarily productive swamp forest with by far the highest density of orangutans - over twice the record number. The animals were the most sociable we'd ever seen: they hang out together, they're nice to each other, they even share food.

And this is an interesting thought:

Q. Were orangutans more social in the past?

A. I guess the rich forest areas that allowed them to live in groups were much more common in the past - they're the ones that are best for rice growing and farming - but there's no way of knowing for sure.

Orangutans and their relatives used to live across a huge swath of East and Southeast Asia, so it is very credible that much of their current habitat on Sumatra and Borneo is actually relatively marginal compared to their former range. Are most of today's orangutans a shadow of a formerly very gregarious species? And how related is their highly arboreal existence to their long life history and exceedingly long interbirth interval? They are a very interesting species from that regard -- a true survivor of the Miocene age of the apes.

From the "any publicity is good publicity" department: Popular Science's list of the worst jobs in science includes "Orangutan-pee collector".

"Have I been pissed on? Yes," says anthropologist Cheryl Knott of Harvard University. Knott is a pioneer of "noninvasive monitoring of steroids through urine sampling." Translation: Look out below! For the past 11 years, Knott and her colleagues have trekked into Gunung Palung National Park in Borneo, Indonesia, in search of the endangered primates. Once a subject is spotted, they deploy plastic sheets like a firemen's rescue trampoline and wait for the tree-swinging apes to go see a man about a mule. For more pee-catching precision, they attach bags to poles and follow beneath the animals. "It's kind of gross when you get hit, but this is the best way to figure out what's going on in their bodies," Knott says.

The short article does point out the great value of the work in wild primate conservation and biology. And it doesn't call them "whiz kids"!

And it is sure seeming easier than job number 3: "Kansas Biology Teacher".