john hawks weblog

paleoanthropology, genetics and evolution

gorillas

  • Mountain gorilla visit

    Sun, 2013-04-21 17:23 -- John Hawks

    Chimpanzee researcher Maureen McCarthy describes a visit to Bwindi Impenetrable Forest in Uganda, to see the mountain gorillas: "Uganda's other great apes".

    Like chimpanzees, gorillas are very closely related to humans and can easily catch the illnesses we carry. Just one outbreak of a respiratory infection could be enough to wipe out an entire gorilla group, or worse.

    Though this may seem like a bleak state of affairs, mountain gorillas are actually heralded as a conservation success story. Their numbers have increased significantly in recent decades as a result of conservation efforts linked to ecotourism. Tourists flock to Uganda each year to visit these famous residents. Now it was our turn.

    McCarthy's earlier posts, sort of a field journal about her work with wild chimpanzees in Uganda, are worth exploring.

  • Quote: Craig Stanford on gorilla habitat threats

    Tue, 2013-01-22 11:02 -- John Hawks

    Primatologist Craig Stanford was interviewed about habitat threats to gorilla populations by a public radio station: "The Human Threat to Great Apes":

    Cell phones, like many other electronic devices, are built with capacitors, which require tantalum extracted from coltan. Eighty percent of the world’s coltan supply is mined in the Democratic Republic of Congo, in the heart of the remaining habitat of eastern lowland gorillas. With an increasing demand for electronics driving a worldwide hunger for coltan, miners in the DRC are polluting and consuming gorilla habitat while extracting the ore. Compounding the problem, miners hunt the apes for food. The situation is grim, and these gorilla populations will go extinct soon without a sustained effort to intervene.

    Cell phones aren't the most common devices with capacitors, but they certainly help to personalize the issue.

  • Quote: Fossey on Louis Leakey's sense of humor

    Tue, 2013-01-15 22:21 -- John Hawks

    Dian Fossey, writing in Gorillas in the Mist about her recruitment to study the mountain gorilla:

    Our conversation ended with his assertion that it was mandatory I should have my appendix removed before venturing into the remote wilderness of the gorillas' high altitude habitat in central Africa. I would have agreed to almost anything at that point and promptly made plans for an appendectomy.

    Some six weeks later on returning home from the hospital sans appendix, I found a letter from Dr. Leakey. It began, "Actully there really isn't any dire need for you to have your appendix removed. That is only my way of testing applicants' determination!" This was my first introduction to Dr. Leakey's unique sense of humor.

  • Darwin's primate phylogeny

    Sat, 2013-01-05 23:24 -- John Hawks

    I'm doing some reading and ran across a 2009 post by Brian Switek ("Darwin, Ardi and the African apes"), who touched on a little-appreciated aspect of Darwin's conception of human relationships:

    Yet there is something else that has long gone overlooked about Darwin’s oft-quoted “African apes” passage. Today we take it to mean that out of all living apes our species shared a recent common ancestry with chimpanzees and gorillas, thus suggesting that humans evolved in Africa. Darwin did not have the details but the consensus is that he turned out to be right in a general sense. In truth, however, Darwin’s conception of human evolution may not have been as modern as we have presumed.

    Darwin manuscript page with primate phylogeny illustrated

    Darwin's 1868 drawing of primate phylogeny. He places "Man" as an outgroup to a 3-way trichotomy of chimpanzee-gorilla, orangutan and Hylobates clades. From the Darwin Online Manuscript Catalogue, digital image copyright Cambridge University.

    As Switek describes, anthropologists often credit Darwin with a very modern conception of primate phylogeny. This credit comes because of a passage in the Descent of Man in which Darwin argues that chimpanzees and gorillas, the African apes, are the closest to people. In the course of my reading of the Descent this year, I will come to that passage and consider it in some detail. The important reason for anthropologists to note that passage is that it directly contradicted Haeckel, whose work on human evolution began earlier than Darwin, and who had claimed that humans are closer to the orangutans than the African apes.

    The drawing above, which Darwin produced in 1868, does not follow the scheme described in the Descent. "Man", at the extreme left in the phylogeny, is a sister group to a three-way trichotomy of chimpanzee-gorilla, orangutan, and Hylobates branches. What I find even more interesting is that Darwin clearly changed the arrangement by reversing the branches with Hylobates and chimpanzee-gorilla written on them. If we take his tree strictly as a phylogeny, in which the topology is determined by the arrangement of the branches, then the left-right positions of these two branches do not matter since the branches form a trichotomy. But it is not obvious that Darwin had in the back of his mind what most undergraduates today think about these trees -- that putting species near each other on the page is a sign that they are more closely related.

    This was a manuscript page in Darwin's notes, and from its context it is clear that Darwin himself was not ready to commit on the subject. The drawing was accompanied by a short description on the reverse side, which reads in part: "Arrangement as far as I can make out by comparing the view of various naturalists ... For myself I have no claim whatever to form an opinion."

    Who were the naturalists on whom Darwin depended? One of them was Haeckel, whose 1868 Natürliche Schöpfungsgeschichte included a phylogeny that connected humans with Hylobates and orangutans as Asian "man-like apes" in opposition to African chimpanzees and gorillas.

    But probably Darwin depended on Thomas Huxley for most of his knowledge of these apes, who had published an extensive description of what was known about orangutans, gibbons, chimpanzees and gorillas up to that time in his 1863 Evidence as to Man's Place in Nature. Huxley did not provide any phylogeny or textual assessment of which of the "man-like apes" may be the closest to humans. Huxley observed that many of the descriptions of these primates were unreliable, and he took the attitude that comparing descriptions across different apes was a way to test their veracity. Reading his text with this in mind, it is easy to take away the feeling that these apes mostly share characteristics with each other that make them different from humans. The exception in Huxley's text is his evocative description of upright posture and gait in gibbons. If one were to take Huxley's description and plot a phylogeny from it, I think it would look like the first version of Darwin's drawing above, with Hylobates placed closer to humans, but not necessarily more closely related to humans.

    This scenario is also consistent with Wallace's 1864 argument about human evolution; that we are a long, independent lineage from other primates that originated as early as the Eocene period.

    As I get to this section of the Descent I'll be looking very carefully at why Darwin shifted his view from this 1868 note.

    Synopsis: 
    Darwin drew a phylogeny of primates. Who knew?
  • Quote: Huxley on traveler's tales and primate discovery

    Sat, 2013-01-05 22:42 -- John Hawks

    Thomas Huxley devoted his 1863 book, Evidence as to Man's Place in Nature, to describing what was then known about the anatomy and biology of the living apes, including gibbons, orangutans, chimpanzees and gorillas. Earlier descriptions of these primates had spawned endless confusion. Huxley showed (brilliantly) how the confusion resulted from incorrect accounts of the primates from travelers and the study by European anatomists of mostly juvenile skeletons carried away shipboard from the tropical homes of these primates. After this long discussion, he wrote, with great charity:

    Once in a generation, a Wallace may be found physically, mentally, and morally qualified to wander unscathed through the tropical wilds of America and of Asia; to form magnificent collections as he wanders; and withal to think out sagaciously the conclusions suggested by his collections: but, to the ordinary explorer or collector, the dense forests of equatorial Asia and Africa, which constitute the favourite habitation of the Orang, the Chimpanzee, and the Gorilla, present difficulties of no ordinary magnitude: and the man who risks his life by even a short visit to the malarious shores of those regions may well be excused if he shrinks from facing the dangers of the interior; if he contents himself with stimulating the industry of the better seasoned natives, and collecting and collating the more or less mythical reports and traditions with which they are too ready to supply him. In such a manner most of the earlier accounts of the habits of the man-like Apes originated; and even now a good deal of what passes current must be admitted to have no very safe foundation.

    I just love the way that passage starts!

  • Perils of talking to apes

    Fri, 2012-09-28 10:28 -- John Hawks

    Barbara King comments on Koko, Kanzi and Panbanisha, "Thoughts On Three Famous 'Language Apes'".

    For decades, the Gorilla Foundation, run by the scientist Penny Patterson, has maintained — based on Koko's own use of sign language — that Koko would like to have a baby. Recently the Foundation posted this video clip, in which Koko is presented, verbally and in diagram form, with four complicated choices about "family planning."

    Patterson, at the end of the clip, affirms her interpretation that Koko grasped all of the options presented to her. The idea is that Koko, by pointing to one of the four diagrammed choices, can and should help make decisions that involve the reproductive activities and the welfare of other gorillas. This raises ethical issues, to say the least.

    We haven't come to the apes in my Biology of Mind course yet, but we were discussing the nineteenth-century origins of ethology yesterday. The initial move toward a science of animal behavior was possible because anthropomorphic accounts of animal behavior were set aside. The apes pose a recurring challenge to the rejection of anthropomorphism, because some of their behavioral capabilities really are homologous with ours. The cognitive border between ape and human may be a no-mans land, with one or two traits occasionally crossing the frontier to the other side. King's last word is fitting -- an ape can never grasp the complexities of the human world...yet neither can we fully grasp the complexities of theirs.

  • Gorilla genomics and hearing evolution

    Thu, 2012-03-08 00:37 -- John Hawks

    The Nature News story on the gorilla genome includes this section relevant to the evolution of hearing in gorillas and humans:

    Some of these rapid changes are puzzling: the gene LOXHD1 is involved in hearing in humans and was therefore thought to be involved in speech, but the gene shows just as much accelerated evolution in the gorilla. “But we know gorillas don’t talk to each other — if they do they’re managing to keep it secret,” says Scally.

    This weakens the connection between the gene and language, says [Wolfgang] Enard. “If you find this in the gorilla, this option is out of the window.”

    This is one of the genes that I have been working on with reference to its acceleration on the human lineage. It is a mistake to view the evolution of hearing to be directed specifically to language; instead human and gorilla lineages are both adapting to an aural environment different from ancestral hominoids. In both these lineages, there was an increase in body size and reduction in the mean frequency of vocalizations, enough to prompt adaptive changes. In humans, we have had additionally the addition of language as a communication system, which has its own auditory requirements. The connection with language is only indirect, in that human-specific changes to this and other genes provide evidence of adaptive change in the auditory system.

  • Meet Gorilla gorilla

    Tue, 2011-09-27 08:15 -- John Hawks
    Synopsis: 
    Introducing the largest living primate, the gorilla.

    The gorilla is the world's largest living primate. Gorillas are presently distributed broadly across West and Central Africa, in forested areas where human activity remains minimal. A small pocket of gorillas survives in the mountains of East Africa.

    The eastern and western gorilla geographic ranges do not touch each other today, and the two areas are home to different subspecies. The western range is the largest area, home to the western lowland gorilla, or Gorilla gorilla gorilla. In the eastern part of the gorilla range, lowland gorillas are called Gorilla gorilla graueri, and the small population of mountain gorillas is Gorilla gorilla beringei. Many biologists would term these as different gorilla species, recognizing their distinct genetic and Like the two subspecies of living orangutans, these gorilla subspecies are substantially different in genetic variation but similar in most aspects of their behavior. Both subspecies are currently threatened with extinction as their habitat disappears and they become exposed to human bush hunting.

    No fossil record of gorilla evolution from the last nine million years is presently known.

    Study the gorilla skeletons at this station and consider their anatomy. What aspects of the gorilla anatomy reflect the large size of these primates? What aspects of the anatomy would be the same even if gorillas were much smaller?

    One way to answer those questions is to compare the male and female gorilla. Compared to other apes, gorillas have the largest degree of sexual dimorphism in body size. Features that are exaggerated in the male gorilla may often be traced to their large size.

  • Scanning the ape fecome

    Mon, 2010-09-27 17:00 -- John Hawks

    Donald McNeil, Jr., has written up some background detail about last week's story that falciparum malaria came from gorillas: "A finding on malaria comes from humble origins". It's one of many research findings coming out of a systematic collection of fecal samples from African ape field projects:

    Dr. Hahn, a virologist at the University of Alabama at Birmingham, is an expert not in malaria but in S.I.V., or simian immunodeficiency virus, the precursor to the virus that causes AIDS in humans. But she has made deals with primate researchers all across Africa who collect fecal samples for their own projects, to have them take extras for her.

    They go into vials with a special solution, called RNAlater, that preserves the nucleic acids of all the cells in the sample — which includes not only what apes eat, but cells sloughed off their gut linings, which contain all the things infecting them. She has systematically sequenced the genes of many of those infective agents: S.I.V., simian foamy virus, hepatitis and now malaria parasites.

    Poop metagenomics. I wonder to what extent pathogens in meat may pass through the gut with DNA intact. Probably not a big issue with African apes, as meat consumption is fairly sporadic even in chimpanzees. But you'd want to be cautious doing certain things with carnivores.

  • Falciparum malaria came from gorillas

    Wed, 2010-09-22 15:38 -- John Hawks

    Malaria in humans is caused by one of five different species of Plasmodium parasites. The deadliest of these is P. falciparum, especially within Africa where native resistance to P. vivax is high. Where the vivax parasites seem to have been around for at least tens of thousands of years, P. falciparum in many ways looks relatively young. Its comparative lack of genetic variation suggests either a recent origin from some other primate species, or an intense bottleneck or selective sweep affecting the parasite's demography. In either case, the falciparum history seems to indicate that its present widespread distribution is a very recent phenomenon -- possibly within the last 5000 years.

    Because P. falciparum is phenotypically similar to the major chimpanzee malaria parasite, P. reichenowi, most scientists have assumed that we got falciparum malaria from chimpanzees. But in a new report, Weimin Liu and colleagues [1] have surveyed parasite variation in gorillas, bonobos and chimpanzees across Africa, finding that human falciparum parasites all group in with a single small clade of gorilla parasites. The other primates carry many varieties of parasites, with typical individuals being highly heteroplasmic -- that is, carrying several different strains.

    From the discussion:

    Using single-template amplification strategies and a much larger collection of ape specimens than previously analysed, we show here that wild-living chimpanzees and western gorillas are naturally infected with at least nine Plasmodium species. Among more than 1,100 SGA-derived mitochondrial, apicoplast and nuclear gene sequences from 80 chimpanzee and 55 gorilla samples, we found a total of nine sequences that were related to P. malariae, P. ovale or P. vivax (Supplementary Table 5). All others grouped within one of six chimpanzee- or gorilla-specific lineages representing distinct Plasmodium species, three of which had not previously been described. Significantly, all currently available human P. falciparum sequences constitute a single lineage nested within the G1 clade of gorilla parasites. This indicates that human P. falciparum is of gorilla origin, and not of chimpanzee9, 10, 12, bonobo11 or ancient human5 origin, and that all known human strains may have resulted from a single cross-species transmission event. What is still unclear is when gorilla P. falciparum entered the human population and whether present-day ape populations represent a source for recurring human infection. It has been suggested that the limited levels of genetic diversity seen at many loci in human P. falciparum reflect a relatively recent selective sweep8. Our data suggest that this bottleneck or ‘Eve event’ was instead the consequence of cross-species transmission of a gorilla parasite. It is difficult to date this event without having reliable dates with which to calibrate the Plasmodium phylogenetic trees.

    What's interesting about the study is the sheer coverage of wild primates, and the application of multiple gene trees, which suggests that this is a recent origin of human parasites instead of introgression and selection of a single gene. I don't know if it makes any difference whether the disease came from gorillas or chimpanzees, but it certainly helps to confirm that it is new and not a long-time coevolution. That explains the burst of recent selection associated with resistance genes, especially within Africa.


    References

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Neandertals

For years, I've worked on their bones. Now I'm working on their genes. Read more about the science studying these ancient people.

Denisova

From a finger bone of an ancient human came the record of a completely unexpected population. My lab is working on the science of the Denisova genome.

Acceleration

The advent of agriculture caused natural selection to speed up greatly in humans. We're uncovering some of the ways that populations have rapidly changed during the last 10,000 years.

Malapa

Just outside Johannesburg, the Malapa site is producing some of the most exciting finds in human evolution. This site is the headquarters of the Malapa Soft Tissue Project.