Showing posts with label primates. Show all posts
Showing posts with label primates. Show all posts

Friday, July 4, 2014

The Bigfoot Question: A Genetic Analysis of Yeti Hair


It’s been a while since I’ve written about Bigfoot, and that’s a shame because he’s pretty fun to write about. As with many things, I like to keep it in a scientific context. That’s why I was pretty stoked to see a recent Sasquatch paper in Proceedings of the Royal Society B. A paper that takes an interesting approach: genetics.

Right off the bat the paper does not assume non-existence, both pointing out that there are numerous reports and sightings yet no bodies or recent fossils. Theories abound about what these animals are, ranging from surviving populations of collateral hominids to unlikely hybrids. As a general rule, modern science shies away from the yeti-finding field, to the point that they make believers feel rejected. Admittedly, believers have point in that science should not accept or reject anything without examining the evidence and testing hypotheses. Pretty much the definition of science, right? So that's what authors Sykes et al. do, take a scientific approach.

The researchers collected a total of 57 Bigfoot hair samples submissions from museum and individual collections. They went about it all officially with a joint press release in May 2012 by Museum of Zoology, Lausanne and the University of Oxford. Then, to eliminate obvious non-hairs, they subjected the samples to macroscopic, microscopic and infrared fluorescence examination. Based on provenance or historic interest, thirty-seven of the samples were selected for genetic analysis. Hairs were first cleaned to remove surface contamination - just consider how many people had handled a sample, so you need to eliminate known human DNA to leave just sample DNA. The meticulously cleaned hair samples were then ground in a buffer to homogenate, incubated with proteinase K, and extracted for PCR amplification. This amplification was of the ribosomal mitrochondrial DNA 12S fragment corresponding to bps 1093-1196 of the human mitrochondrial genome, using a permissive primer combination that allows for a wide range of mammalian DNA. The results were then compared to GenBank accessions for species identification.

Perhaps it is important to point out what the 12S mitochondrial DNA is and how it works. Even within fur-bearing species, there is a large amount of variation in hair appearance that can be identified under the microscope to determine species. But, in the absence of an experienced hair examiner (yes, those exist), a reliable, alternative analysis must be used. This analysis comes in the form of highly conserved mitochondrial DNA regions, these are particular sequences that have been maintained by evolution despite speciation, probably because they are functional. Mitochondrial 12S ribosomal RNA has an amplification size that renders it useful for even problematic and/or degraded samples. Highly conserved primer regions and the high nucleotide species diversity present within the portion of the 12S gene examined allows for identification at least to genus and often species. Studies examining the extent of 12S homology within and between species have shown a high degree of confidence in the test's ability to match species from biological samples, usually hair. This includes primate homologies like the chimpanzee, who shares a 98% homology with the human 12S region, Gorilla (97%) and rhesus macaque (90%). These studies have shown that it is unlikely that a non-human primate hair could be confused with human hair using this system.

Now knowing all of this, back to the results of the Bigfoot study. Despite multiple attempts, seven of the samples yielded no DNA sequences, leaving the researchers with 30 samples. These 30 samples were each matched to a known species. Ten belonged to various bear species, four were cows, four were horse, four were wolves/dogs, two were raccoons, one was a deer, one a Malaysian tapir, one a sheep, one a serow, and one was human (exact match).

There has been quite a few articles in the news about this study, and that’s good because this paper is a nice example of using hard science to test a theory. It is also works towards bridging the gap between two rather disparate groups of people. So kudos to you Sykes et al.


ResearchBlogging.orgSykes, B., Mullis, R., Hagenmuller, C., Melton, T., & Sartori, M. (2014). Genetic analysis of hair samples attributed to yeti, bigfoot and other anomalous primates Proceedings of the Royal Society B: Biological Sciences, 281 (1789), 20140161-20140161 DOI: 10.1098/rspb.2014.0161

A nice write-up from Science News "'Bigfoot' samples analyzed in lab"

For more on 12S see an article in Forensic Magazine titled "Easy Species DNA Identification for the Forensic Laboratory Using 12S Mitochondrial DNA"


(images via WhoFortedBlog, NewEngland BioLabs, Nature Reviews Genetic paper DOI:10.1038/nrg1606, respectively)

Friday, January 11, 2013

The Silverback Playbook: Changing Climate and Ape Distribution


On occasion, I go back to my roots in biogeography and peruse that subset of journals for interesting articles. Admittedly, I now skip over some topics that I used to devour, such as the species-area relationship (the "most general, yet protean pattern" that has recently warranted a special virtual issue). These days, I tend to stop and read articles about distribution patterns, especially as they relate to current problems like climate change.

There are an increasing number of studies that show that climate change will affect species distribution patterns and biodiversity patterns in general. Temperatures, rainfall patterns, sea level changes, etc. are likely to cause geographic shifts in the ranges of plants and animals, altering their relationships with the environment and other species. The common methods for predicting these effects are called bioclimatic envelope models. Basically, these models try to determine the "climate envelope," a description of the climate that defines a species' range, and then map the geographic shift of that envelope under climate change. These types of models are useful for predicting distribution patterns, but they do not inform us about the underlying mechanisms that limit species' distribution and how species will change their behavior and/or the kinds of habitats where they can survive. Think about this behavior part a little more in depth, specifically taking brain size into account. It has been shown that large-brained species are better able to cope with seasonal changes in their environments, buffering themselves against modest levels of climate change, and are more resistant to extinction.

When you think of large-brained species, which ones come to mind? Probably the primates, specifically the African apes (gorillas and chimpanzees). What do we already know about these species? We know that they live in Africa (the most vulnerable of all continents to the effects of climate change), occur in similar habitats (although they differ somewhat in biogeographical ranges), are highly endangered, have highly restricted ranges, have a slow life history, have a large body mass, and have somewhat similar diets. Knowing this, how do you think climate change will affect them?

A study published in the Journal of Biogeography takes a look at how the behavior and distribution of African apes will be affected by climate change. They use a time budget model to investigate how climate warming and behavioral flexibility might affect ape survival. Time budget models are based on individual behavior, how much of an individual animal's time is spent on feeding, resting, traveling and socializing. An animal's time is limited (there is only so much time in a day) and so there is a constraint on the size of a group that can be maintained in a particular habitat which ultimately determines a species' distribution. These types of models can predict distribution as well as the bioclimatic envelope models, as they are based on simple climatological variables, with the added advantage of providing informing us about mechanisms of keeping a species in a particular habitat and evaluating the level of ecological stress in areas where it does occur. They applied this model to data from 20 natural populations of gorillas (Gorilla beringei and Gorilla gorilla) and chimpanzees (Pan troglodytes and Pan paniscus). The model looked at the relationship between climate, group size, body weight, and time budgets. They ran the model to predict ape distribution across Africa under a uniform worst-case climate change scenario, highlighting the importance of individual behavioral requirements for survival. I'm going to save you lengthy descriptions of the model parameters, time budget equations, and model testing. You can thank me later.

The study found that gorillas are more restricted by temperature variation than are chimpanzees. This may cause gorillas to suffer more strongly from the effects of global warming. Their larger body mass and smaller group sizes also increase their risk of extinction even with their behavioral flexibility. This doesn't mean that the chimps are unaffected. They found that chimpanzee communities will be significantly reduced even at locations where they are predicted to survive. The model showed that two critical factors may ultimately determine their survival at these locations: minimum viable community size and minimum party size. Although the distribution for both genera is in the downward direction, the two taxa are predicted to respond differently to changes in climate. Chimpanzees are expected to primarily suffer a reduction in community size because they will need to spend an increasing amount of their time moving and resting. And considering that minimum viable community size is one of the two critical factors, chimps will find it difficult to survive in any of their present habitats and may even go extinct. On the other hand, gorillas already live in small groups and when combined with a dramatic reduction in available habitat (again with the moving and resting time), climate change is predicted to have a stronger effect on their biogeography. However, the authors think that the few surviving populations should be able to maintain present-day group sizes, making them locally stable. Even if the changes in climate were not as extreme, the researchers think that their model would still predict that apes will suffer habitat loss simply due to time budgeting problems that may be reinforced by indirect effects (like temperature on leaf quality). Sure, behavioral flexibility may help, particularly with the more socially fluid chimpanzees, but the environment will support only what it can support (especially for hungry, large bodied creatures).

It is important to note that this study does not include anthropogenic (human caused) influences. Couple those with the doom-and-gloom predictions that the study already makes and it looks like it's bye-bye time for the big apes. That is a bit of a depressing note to leave the post on. Perhaps the good (or happy?) note to leave on is that studies such as these (that take mechanism into account) can give us better ways to predict and preserve optimal habitats, ultimately finding ways to best conserve these species. After all, that is the goal right?


ResearchBlogging.orgLehmann, J., Korstjens, A., & Dunbar, R. (2010). Apes in a changing world - the effects of global warming on the behaviour and distribution of African apes Journal of Biogeography, 37 (12), 2217-2231 DOI: 10.1111/j.1365-2699.2010.02373.x


(image via earthtimes.org)
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