john hawks weblog

paleoanthropology, genetics and evolution

Flores

  • Miocene hominids and a crisis of confidence

    Fri, 2007-06-29 12:47 -- John Hawks

    Out of this week's Science Times special on evolution, I clicked into John Noble Wilford's article first, titled "The Human Family Tree Has Become a Bush With Many Branches".

    Now, I don't know about you, but that seems like a boring headline to me. They've been talking about human evolution being a bush for going on 20 years now. It was an old idea when I was in graduate school. So it seems like, if this is all we have going on, the "new frontier" of paleoanthropology must be pretty dull.

    The writer doesn't write the headlines, and the headline doesn't describe Wilford's story, which is basically a verbal slide show of fossil discoveries over the last decade or so. Some bone pictures (of the actual species discussed) accompany the article, and it's a good enough sort of account of new finds since 1990, framed around the tension between fossil finders and molecule mavens.

    But I'll be a little critical. The thesis is that paleoanthropologists suffered a crisis of confidence after molecular data came online in the 1980's, and "a rapid succession of fossil discoveries since the early 1990's has restored" it.

    Well, OK, maybe. But consider the listed discoveries: Kenyanthropus, Ardipithecus ramidus, Ardipithecus ramidus, Orrorin tugenensis, Sahelanthropus tchadensis, Homo floresiensis, and Australopithecus anamensis. Of all of these, only Ar. ramidus and Au. anamensis have gone without significant controversy.

    We can set aside H. floresiensis for a moment -- the controversy about it being possibly the loudest, it also stands apart as the only species listed younger than 3.9 million years. All of these early Pliocene and Miocene species have also been challenged -- by the discoverers of the others, by old hands, and by young upstarts like me. At least one research group has claimed that all of the Miocene "genera" may actually belong to one species. Another has claimed that most of these "hominids" may actually be apes.

    Whether there was any crisis of confidence among paleoanthropologists, all this disagreement is certainly business as usual.

    And, contrary to the article, every one of these species would be thrown from the hominid line, if we believe the molecules. Here's the text from the article:

    Genetic clues also set the approximate time of the divergence of the human lineage from a common ancestor with apes: between six million and eight million years ago.

    Fossil researchers were skeptical at first, a reaction colored perhaps by their dismay at finding scientific poachers on their turf. These paleoanthropologists contended that the biologists' "molecular clocks" were unreliable, and in some cases they were, though apparently not to a significant degree.

    ...

    The new finds have filled in some of the yawning gaps in the fossil record. They have doubled the record's time span from 3.5 million back almost to 7 million years ago and more than doubled the number of earliest known hominid species. The teeth and bone fragments suggest the form -- the morphology -- of these ancestors that lived presumably just this side of the human-ape split.

    It is true that the new fossils date as far back as 7 million years; with Sahelanthropus just under that date, Orrorin at around 6 million, Ar. kadabba at 5.5, Ar. ramidus at 4.4, and Au. anamensis at around 4.1.

    But it has been many years since a genetic comparison indicated a human-chimpanzee common ancestor as old as 6-8 million years. This year's study by Holbolth et al. (2007) estimated a human-chimpanzee speciation time of 4.1 +/- 0.4 million years. That makes Au. anamensis possibly too young to be a hominid. The rest of those species would presumably be just so many apes.

    Now, I don't believe for a second that Au. anamensis is an ape and not a hominid. It just looks too much like Au. afarensis -- so much so that some would put them in the same species. The evolutionary transition between these two is well documented, and will be more so when some as-yet-unpublished fossils come out. So anything younger than 4.1 million years is almost certainly not right for the human-chimpanzee divergence.

    But the 4.1 million year estimate is not unusual compared to other recent studies. My post from last May covers many of these recent studies, including last year's problematic "hominid-chimpanzee hybrid speciation" paper by Nick Patterson and colleagues. The conclusion in that paper about hybridization was certainly wrong, but the date of 5 million years was right in line with other estimates.

    These genetic comparisons are not easily dismissed. Possibly there has been a rate deceleration of mutations in the human lineage that means that the estimated dates are too recent. Maybe 4.1 million years can be stretched into 6 million. Maybe it can even be stretched into 7 million. But all this stretching does have other effects -- on the estimated dates of earlier divergences -- and those are compounded by a large multiple of the few million years we may try to push the human-chimpanzee speciation date. That 4.1 million year estimate is calibrated from an African-Asian great ape divergence at 18 million years ago. Push the human-chimpanzee divergence to 7 million, and you push the orangutan-human divergence back into the Oligocene. Are silent sites in humans evolving more slowly than cercopithecines? Probably. Are they evolving that much slower than orangutans? I suppose nothing is impossible, but maybe we should take another look at those fossils.

    All this is to point out that there really is a conflict between these Miocene "hominids" and genomic evidence about human-chimpanzee speciation time. I don't see any magic solution to this problem from the molecular side -- those dates keep coming up again and again from different regions, and from comparisons across many regions -- including estimates that are not calibrated by other fossil divergences. This is not an easy "the molecular clock must be wrong" kind of problem.

    Nor are the fossils an easy problem. There is pretty good evidence for vertical posture or hindlimb-dominant movement in all of these "hominids." Up to now, we've accepted these kinds of features as de facto evidence of bipedality, and assumed that bipedality is such a unique character of hominids that it is unlikely to be any older. Yet few of these fossils provide really good evidence for obligate bipedality, and some of them provide none at all.

    Is it possible that bipedal apes long preceded the divergence of humans and chimpanzees? Was the common ancestor of the two lineages a biped? Or was significant vertical posture a common feature of many Miocene apes -- making Sahelanthropus a possible homologue of Oreopithecus?

    Which feature is the important one? The long nuchal plane of Sahelanthropus? The femur neck cortical bone distribution of Orrorin? The toe bone of Ar. kadabba? Heck, I can hardly convince my undergraduates about that toe bone!

    I've talked to people about this. Some think that all the molecular stuff is just jibberjabbing, and any day now we will find out that the date estimates were wrong all along.

    I think it may be time to start doubting our confidence again.

    UPDATE (6/28/2007): I've gotten into rather an interesting e-mail discussion about whether I should have included Homo georgicus on the list of new species. Frankly it didn't occur to me: Wilford didn't mention it.

    Actually if you start to think about all the new names that have been proposed in the last 15 years, it is a quite bushy list. It will be no surprise that I think this bushiness has more to do with the listers than the listees.

    Anyway, there is something interesting about early Homo right now that goes beyond the simple splitter/lumper questions. I'll have more to say about it in a few days.

    References:

    Hobolth A, Christensen OF, Mailund T, Schierup MH. 2007. Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet 3:e7. doi:10.1371/journal.pgen.0030007

    Patterson N, Richter DJ, Gnerre S, Lander ES, Reich D. 2006. Genetic evidence for complex speciation of humans and chimpanzees. Nature 441:1103-1108doi:10.1038/nature04789

    Tags: 
    Ardipithecus
    A. afarensis
    Kenyanthropus
    genetic divergence
    A. anamensis
    Flores
    Miocene
    Sahelanthropus
    Pliocene
    Orrorin

  • Ancient DNA profile

    Wed, 2007-06-27 20:16 -- John Hawks

    An article by science writer Henry Nicholls in PLoS Biology covers a lot of ground. Most of the attention goes to Alan Cooper, with Svante Pääbo in a supporting role. There is this on the hobbits:

    aDNA could also, in principle, be used to shed light on the evolutionary position of the 18,000-year-old "hobbit" recently unearthed on the Indonesian island of Flores [8]. Both Cooper and Pääbo have offered to have a go at isolating DNA from the "hominid" skeleton, but the early signs are that DNA has not survived. "The somewhat moist and tropical preservation conditions make the recovery of DNA improbable," says Peter Brown, the paleoanthropologist at the University of New England in Armidale, Australia, who led the hobbit study. Efforts to extract DNA from other bones collected at the same site as this tiny hominid have not produced results. "We have made attempts with Stegodon molars," he says, "but so far without success."

    I am most impressed with studies that survey many ancient specimens to make conclusions about ancient population dynamics, such as local extinctions and recolonizations. The recent arctic fox paper is a great example. This article mentions two more: a study of ancient bison fossils from Beringia, and a study of arctic brown bears. Here's a paragraph about the bison study:

    Cooper's latest work has analysed DNA from over 400 bison fossils from Beringia—the frozen wastes between eastern Siberia and the Canadian Northwest Territories [3]. "What we've done is carbon-date a shitload [JH --is that a metric shitload?] of bison and get DNA out of them." It's the largest aDNA study to date, he says (Figure 1). The icy conditions mean that good quality mitochondrial DNA could be extracted from most of the specimens. The bison could also be dated accurately. This allowed Cooper and his colleagues to trace the changes in the bison genetic diversity from 150,000 years ago to the present. It was even possible to predict the effective population size throughout this period of bison evolution. "Our analyses depict a large diverse population living throughout Beringia until around 37,000 years before the present, when the population's genetic diversity began to decline dramatically," they note.

    The main drawback of these studies has been their limitation to mitochondrial DNA. The story of that one molecule is informative, but it is not the whole story -- and in particular, it may reflect selection associated with climate change, not just extinction and population expansion.

    That is the main reason the Neanderthal genome is so important -- it allows us to compare the vast majority of the genome to find evidence of functional changes. Likewise, the ability to look at many genetic regions is a highlight of the described work on early maize domestication:

    Pääbo's analysis suggests that the alleles typical of contemporary maize were already present in Mexican maize 4,400 years ago, so just a couple of thousand years after its initial domestication from the wild grass teosinte (Figure 3). "Quite early on, properties were selected that were not only the structure of the plant but also the biochemistry," he says.

    There is really a light year of difference between the labs bringing out nuclear genomic sequences and those working exclusively with mtDNA. There is so much more information to be had from the full genome that these datasets will keep PhD's busy for decades.

    But for the time being, labs that limit to mtDNA are able to bring out more and more sequences from different individuals. This adds the essential component of population variability, which is essential to understanding the dynamics of evolutionary change. So it's like we are getting a third of the story from each of these sides -- with the other third coming, of course, from traditional morphological comparisons.

    References:

    Nicholls H. 2005. Ancient DNA Comes of Age. PLoS Biol 3: e56. doi:10.1371/journal.pbio.0030056

    Tags: 
    ancient DNA
    Neandertals
    Flores

  • Answers in the New York Times

    Fri, 2007-05-25 12:19 -- John Hawks

    So I was reading yesterday's total softball exhibition review in the New York Times, on the new Ken Ham-built Creation Museum:

    For the skeptic the wonder is at a strange universe shaped by elaborate arguments, strong convictions and intermittent invocations of scientific principle. For the believer, it seems, this museum provides a kind of relief: Finally the world is being shown as it really is, without the distortions of secularism and natural selection.

    I mean, really softball:

    The Creation Museum offers an alternate world that has its fascinations, even for a skeptic wary of the effect of so many unanswered assertions. He leaves feeling a bit like Adam emerging from Eden, all the world before him, freshly amazed at its strangeness and extravagant peculiarities.

    You see, all freshness and light. But aside from being fantastically wrong, the thing sounds very creepy. I mean, it's like a Simpsons parody of itself:

    Start accepting evolution or an ancient Earth, and the result is like the giant wrecking ball, labeled "Millions of Years," that is shown smashing the ground at the foundation of a church, the cracks reaching across the gallery to a model of a home in which videos demonstrate the imminence of moral dissolution. A teenager is shown sitting at a computer; he is, we are told, looking at pornography.

    Clearly, the teenager is teenage Milhouse!

    Well, the article is fairly clever, but not in the least bit critical of all this nonsense. Wondering who wrote it, I looked -- Edward Rothstein, the arts and culture reporter.

    So I got to thinking, hmmm.... Why did the Times send their culture reporter to cover this museum in such a friendly way, when they assigned science reporter John Noble Wilford to cover this year's opening of the new Human Origins Hall at the American Museum of Natural History? I mean, they're on the same subject, right? Shouldn't they get the same reviewer?

    Huh. So I got a little interested in what else Rothstein had written lately. I mean, didn't his trip on the Grand Canyon skywalk give him some insight into the Creation Museum's claim that it formed in 40 days and 40 nights?

    And then I saw Rothstein's article from today's paper -- reviewing another new exhibit at the AMNH:

    They lure children into dank swamps and devour them. They live in caves or among high rocks or deep in dense forests. They are covered with scales or thick fur. They have hands at the ends of their tails or a single glaring eye. They exhale fire, cause hurricanes with their wings or feast on human eyes, teeth and nails. They might also whimsically help the unwitting, but they are almost all mercurial, unreliable, tricksters.

    Such are the mythic creatures of our earth.

    Henry Gee's fantastic creature

    The AMNH unicorn. Don't tell Henry Gee!

    Ah-ha! This is all becoming clear now. The Times wasn't really softballing the Answers in Genesis museum. It's just that Rothstein covers the unicorn and dragon beat!

    How else to explain the uncanny similarities between these articles? For example, here is a passage from the Creation Museum review:

    It is a measure of the museum's daring that dinosaurs and fossils — once considered major challenges to belief in the Bible's creation story — are here so central, appearing not as tests of faith, as one religious authority once surmised, but as creatures no different from the giraffes and cats that still walk the earth. Fossils, the museum teaches, are no older than Noah's flood; in fact dinosaurs were on the ark.

    And here is a passage from today's "Mythic Creatures" review:

    But these mythic creatures are actually transformations of real creatures glimpsed but barely understood. A sea serpent might be simulated by enormous schools of large fish leaping in the waves, the rise and fall of their bodies seeming to be knit into an enormous undulating being; turn a wheel at the exhibition, and miniature dolphins leap in the waves in a display case, appearing to form a single organism.

    The kraken might have evolved from sightings of enormous squids, one of which was recently found in New Zealand, with single arms over 19 feet long. Nature sometimes trumps the human imagination.

    OK, I admit it's confusing. One museum teaches mythology as science, another teaches mythology transformed by science. Read both reviews and see which is more interesting.

    Tags: 
    Flores
    creationism

  • Island hopping

    Sat, 2007-05-12 15:42 -- John Hawks

    This article from The Age lays out an ambitious excavation schedule for Mike Morwood and colleagues:

    Professor Morwood, with a team headed by Indonesian archaeological professor Fachroel Aziz from Indonesia's Geological Survey Institute, will soon start excavations in the Atambua Basin of Timor. Afterwards, the team will begin diggings in Sulawesi and will return to the Ling [sic] Bua cave in Flores, where the hobbit species was uncovered.

    "We predict a number of these islands are probably going to have their own endemic human species, and many of them will be small," Professor Morwood, from the University of Wollongong, said.

    The article spends some words on size differences in island animals, raises the issue of island gigantism (hmm...does this mean we'll see the return of Meganthropus?), and this:

    Professor Morwood flagged that any new human species found on Timor and Sulawesi would be called Homo timoriensis and Homo celebesiensis (Celebes being the former name of Sulawesi).

    That just seems like a missed opportunity. If it were me, I would sell the naming rights to the highest corporate bidder. How about "Homo pizzahutiana". Ooh ooh! "Pan crusti!" You could probably get money for at least 20 field seasons out of them.

    How sustainable was "seafaring"?

    I've already heard from some correspondents (many thanks!) who consider it hubristic to predict the finding of more human species in Wallacea, when the case for one is still in doubt.

    Maybe so. I think that Sulawesi and Timor, in addition to other islands including Sumba and Sumbawa, may provide an important test. The reason? Seafaring.

    I haven't seen anyone comment on the seafaring issue much since the Liang Bua remains were reported. Recall that when Lower to Middle Pleistocene stone tools were originally found on Flores (from the Soa Basin), their principal importance was documenting some kind of water-crossing technology in early Homo before 800,000 years ago. That was news — with no such evidence anywhere else in the world — and was subject to some controversy.

    Just how good did the "seafaring" technology have to be to establish an occupation on Flores? There were at least two water crossings (Lombok and Sape Straits) of more than 10 kilometers. Robert Bednarik has conducted a series of experiments (the First Mariners Project) attempting to assess the technological requirements for such crossings.

    If the seagoing technology that allowed crossings of these straits was maintained for a long time, it surely should bolster our opinion of the cultural capabilities of the hominids. A raft -- even a simple raft made out of bamboo -- is a complicated compound tool; a tool that involves many pieces put together in a series of steps. Even though many of the steps may be completely identical to each other (that is, lash logs together, repeat), still a raft requires joining dozens of different elements on a single plan, in pursuit of a single non-immediate goal. The creation of such an object would have required a sustained, goal-oriented and design-directed cognition.

    Last year, I wrote:

    [W]hat happened on Timor? It seems to me that the game is over if humans were on Timor in the Middle Pleistocene. There is some indication that they were. If Homo erectus could manage sea crossings to that extent further east than Flores, then there is no way that Flores was a single, unique colonization. With an occupied Timor, we have to assume that regular contacts between Flores and mainland Asia were probable.

    Much depends on what the people were doing with watercraft -- were they using them for fishing? River crossings? Short island-hopping? Ecologies that encourage the use of watercraft exist in the region today, for all of these reasons and more. We can infer that if people were capable of exploiting these ecologies in the past, then the opportunity to do so would have been recurrently (or constantly) present during the last 800,000 years. Like any cultural tradition, seagoing rafts might have been lost over time. But even if people forgot how to make watercraft, the fact that they could invent them in the first place suggests that they should have invented them repeatedly. Humans certainly have done so recently.

    The paradox is that regular crossings of the straits would have prevented isolation of the island populations. It would seem that the hypothesis of isolation entails that seagoing technology was not a sustainable development, and that the initial occupation of Flores (and by extension, Lombok and Sumbawa) was a matter of chance. If this is true, then early evidence of water crossings itself has little, if any, import to our interpretation of early human cognitive evolution.

    Consider that other than this evidence for crossing the Lombok and Sape Straits, there is no evidence for compound tools of any kind before the Middle Paleolithic-Middle Stone Age. If Lower Pleistocene humans were capable of making a raft, this would be a major addition to the evidence for their technological competence.

    Well, I don't know the answer, but I think that finding hominids on Timor would pretty much end the story in favor of more capable seafaring rather than less.

    Sulawesi is less certain; it may have been too easy to get there by chance to really establish that water crossings were controlled and sustained. Sulawesi seems like a great prospect for hominid occupation; the fauna is more Asian than Flores, so it must have been comparatively easier to make the crossing. The Makassar Strait probably was not narrower than the corresponding water crossings from Bali to Lombok and Sumbawa to Komodo, but the opposing coastlines of Sunda and Sulawesi were very long, perhaps providing a greater chance of making a successful crossing without being washed clear of landfall. Of course, that makes isolation much less likely also.

    The more regular water crossings were, the less likely isolation on Flores would have been. It's certainly important to look for hominids on those islands, but maybe not for the reasons everyone seems to be assuming.

    Tags: 
    Middle Pleistocene
    Homo erectus
    Flores

  • A guide to fantasy science

    Thu, 2007-04-26 22:10 -- John Hawks

    I'm about two-thirds of the way through Mike Morwood's new book, The Discovery of the Hobbit, and I'll be posting a review when I'm through. Generally, I have a positive opinion of the book so far.

    Henry Gee has reviewed the book in this week's issue of Nature. I wanted to point out my generally positive attitude about the book, so that you'll know that my miserable opinion of Gee's review has little to do with the book's merits.

    Consider how Gee starts his review:

    The unicorn, wrote Jorge Luis Borges (in Kafka and His Precursors), is universally regarded as a supernatural being of good omen. But there's a problem: despite its folkloric familiarity, we wouldn't know how to recognize a unicorn if we met one in real life. It "does not figure among the domestic beasts, it is not always easy to find, it does not lend itself to classification," Borges continues. "It is not like the horse or the bull, the wolf or the deer. In such conditions, we could be face to face with a unicorn and not know for certain what it was."

    Is Gee smoking crack? What kind of blather is this?

    First of all, I know I'm being terribly literal, but a unicorn is a horse with a horn. One horn. Not so hard to recognize! Maybe my 3-year-old daughters could help edit at Nature.

    Let's see, where have I seen one of those that Gee might recognize? Oh, yeah:

    UK Pound coins with unicorn prominently visible

    Photo credit: Simon Stratford (via stock.xchng)

    There it is, sound as a pound.

    Next, Gee spends several paragraphs expositing on his own role in the publication of the Homo floresiensis announcement. We learn some interesting little facts, like how the authors wanted to name the species "Sundanthropus floresianus" until a reviewer pointed out that future students would confuse the name with a flowery butt.

    I kid you not. Nature has a layer of reviewers to take tushie references out of taxonomy. Somehow they can't tell a left femur from a right, but they're on the watch for sphincter-species!

    The review is entirely self-serving -- there are only three paragraphs that include any reference to the book! In the midst of this babbling about unicorns and hobbits, Gee tells us that skepticism at new hominid discoveries should be dismissed as the predictable result of "mindsets" of the skeptics:

    Such reaction is common in the wake of new hominid discoveries, which are routinely dismissed either as pathological humans (Homo neanderthalensis) or apes (Australopithecus africanus and Sahelanthropus tchadensis). Such reactions say less about the facts than the mindsets of commentators, who might be unwilling to have their comfortable views of the world so forcibly changed. Confronted with what might be a genuine unicorn, many would prefer to see a pantomime horse with a spike glued to its head.

    Ooooh! Since I'm one who has been notably skeptical of Sahelanthropus and have approached H. floresiensis skeptically, I'm obviously a prime target for this paragraph. It is so comfortable to stay in my view of the world where hominids interbreed with each other. Clearly, a bestiary that includes small-brained island bipeds must shake me out of my comfort zone.

    How could I have been so wrong! When every species ever proposed has faced the same resistance? Sure, Tim White says that Kenyanthropus is a glued-together matrix-filled A. afarensis, but that's just his mindset. Or how about Eoanthropus? Sure, Franz Weidenreich thought that it was just a concoction by "English authors," but couldn't he tell that it was more than just a pantomime skull with an orangutan jaw? Why couldn't I see that these petty minds were just holding back the important work of taxonomy!

    No, no, no. You see, if we approach things skeptically, we won't dare to dream about the unicorns:

    The unicorn remains as it always did, frustratingly elusive. This year, the researchers will return to Liang Bua to see if they can discover more. But stories such as this demand a mythological beast altogether less serene. It is as if the researchers had set out to discover some new form of fossil mouse, only to find that they had grabbed a dragon by the tail instead. And as any devotee of Harry Potter will remind you: Draco dormiens nunquam titillandus.

    The theme of the review is perhaps to be expected from Gee, otherwise known as the author of The Science of Middle-Earth. But I find his mixture of fantasy and science to be especially malaprop in the context of the Flores fossils, since with every fantasy word he detracts from the credibility of the journal's review process!

    Some of you will have seen the episode of The Simpsons, titled "Lisa the Skeptic," where Lisa excavates an "angel" from the ground. Here's part of the synopsis from Wikipedia:

    As Homer attempts to get a motor boat, a new shopping mall in Springfield is being built on an area where a large number of fossils were found. Lisa condemns and protests the building of the mall. Thanks to her protest, it prompts the school to conduct an archaeological dig. When Lisa is digging, it reveals a human skeleton with wings. Springfield's residents are convinced it is an angel, and Homer cashes in by moving the skeleton into the family's garage; however, Lisa is skeptical, believing it may not actually be an angel, and even has Stephen Jay Gould test a sample of the skeleton. The next day, Dr Gould runs to the Simpson house and said the tests came out inconclusive and after Lisa on television compares belief in angels to belief in unicorns and leprechauns, Springfield's religious zealots riot and destroy all of the scientific institutions.

    Later, we find out that the "angel" is a publicity stunt for the new mall; Guest voice Gould confesses that he never really performed any tests on the "angel". This is one of my favorite episodes: it's a rare one where Lisa's preachy skepticism is entirely justified, and the "expert" doesn't care enough to do anything at all.

    Now I know, that the episode was missing a scientific editor to encourage Lisa to forget about her doubts, and just to accept the "angel" for what it is. After all, every new discovery has its skeptics.

    Well, there is a lesson to take away from all the unicorn talk. If you are in Cardiff and find the skeleton of a giant, be sure to send your report to Nature, where you'll find a receptive editor. Despite what they may say, there's not one of those born every minute.

    UPDATE (4/26/2007): A reader e-mails, "Remember that Borges was blind." True. Perhaps we can extend this analogy further?

    Another reader: "Well, at least we can expect a fair set of reviews on the Sahelanthropus postcrania...D'oh!"

    References:

    Gee H. 2007. In a hole in the ground.... Nature 446:979-980. doi:10.1038/446979a

    Tags: 
    Sahelanthropus
    Flores
    Neandertals
    A. afarensis
    A. africanus
    Kenyanthropus

  • Women in human evolution reviewed

    Wed, 2007-04-18 11:09 -- John Hawks

    James Adovasio, Olga Soffer and Jake Page have a new book entitled, The Invisible Sex: Uncovering the True Roles of Women in Prehistory. The authors are well-known for their work in both New World and Old World archaeology. In particular, the joint work by Adovasio and Soffer has uncovered evidence for the earliest fabrics and fiber technology, and has led to new interpretations for the famous "Venus" figurines from the European Upper Paleolithic.

    I ran across a nice long review of the book by Laura Miller at Salon.com. It's free if you watch their ads, and the review is full of clever observations. Here's a sample:

    Their point is that, like Hollywood action films, many early conceptions of prehistoric life were fantasies, the work of anthropologists caught up in a thrillingly macho vision of our forebears that owes more to Conan the Barbarian than to the archaeological record. That vision rarely featured women, and when they did appear it was only to sit around awaiting the next delivery of mammoth steaks, for which, it was implied, they would trade their sexual favors or perhaps the handful of nuts and berries they'd rustled up on the side. So seductive is this "theme of man the hunter" that it prevailed when the remains of a diminutive new species of the genus Homo were discovered on the Indonesian island of Flores in 2004 (and promptly labeled "hobbits" by the press). An artist's drawing of the creature depicted it as bearded fellow holding a spear and carrying a freshly slain giant rat slung over his shoulder -- despite the fact that the chief find was a female.

    The review notes that the book also covers the anatomical constraints of the birth process in humans and their implications for cultural assistance with birth -- that's drawn from work by Karen Rosenberg and Wenda Trevathan (quick summary here) -- and I happened to have lectured about it today. It's very important stuff in terms of human life history strategies, and it is likely tied in with the evolution of the human brain. So anatomically speaking, women are central!

    I hope to write more about this book when I get a chance to read it -- Soffer and Adovasio have been really important in reframing our understanding of sex roles in the past, and this looks like an interesting contribution.

    Tags: 
    Upper Paleolithic
    Flores
    archaeology

  • The island rule

    Sat, 2007-04-14 15:13 -- John Hawks

    Mark Lomolino has been one of the central figures in recent work on body size, energetics, and evolution -- especially with respect to the evolution of body size in island species. With several of his colleagues, he had an editorial in the Journal of Biogeography last year, calling for a renewed research agenda in ecogeographical rules -- that is, rules relating body size and other characters to biogeographic variation of different kinds. The island rule is one such rule, other examples are Bergmann's and Allen's rules (relating body size and limb lengths with temperature) and Rapoport's rule (relating north-south species range extents with actual latitude).

    Most of the possibility for a substantial renewal has come from the increased exchange and computerized search capacity for basic observations on body size and shape in different species. The editorial mainly reviews the prospects for developing new theoretical understandings of these rules and their exceptions using new data, and points to the necessity of the comparative approach.

    The editorial treats the island rule as a case study -- and it is probably the best one possible because of the substantial density of recent research on the topic. The authors provide a nice nutshell history of the development of the island rule as a scientific explanation:

    Here we first summarize the epistemology of the island rule as an illustrative case study. This pattern was first described by Foster (1963, 1964), but it was not labelled as a rule (and one 'with fewer exceptions than any other ecotypic rule in animals') until Van Valen's papers in 1973 (Van Valen, 1973a,b: p. 35). Originally, Foster described the pattern as a tendency for different taxa (orders of mammals) to exhibit different evolutionary trends on islands, rodents tending to increase, and carnivores and ungulates tending to decrease in body size. Later, Heaney (1978), Lomolino (1985) and others reinterpreted the rule to be a graded trend from gigantism in the smaller species to dwarfism in the larger species of mammals. This recasting of the island rule reflected the heuristic tension between process and pattern, and theory and empiricism. The earliest articulation of the island rule suggested disparate evolutionary trends among mammalian orders, but this was soon found to be inconsistent with modern evolutionary theory. Rather than invoking some overriding importance of phylogenetic inertia that somehow differs among mammalian orders, the island rule (sensu nova) instead is inferred to reflect differences in selective pressures on islands and among species of different body size (therefore the graded trend should occur within, as well as among, mammalian orders; see explanations by Heaney, 1978; Lomolino, 1985, 2005; Adler & Levins, 1994; Adler, 1996; Marquet & Taper, 1998; McNab, 2001, 2002; Gould & MacFadden, 2004). Note, however, that the geographical context of the island rule's primary pattern is typically limited and binary: terrestrial populations occur in just two types of ecosystem, islands or mainland sites. Yet we know that islands vary in area, isolation, latitude and other characteristics that influence the abilities of organisms to colonize and maintain populations. Thus, in addition to the primary pattern, body size of insular populations of particular species should not be constant, but should vary in a non-random manner among islands and archipelagoes. These secondary or corollary patterns provide excellent opportunities to evaluate alternative explanations for the island rule, for example by testing for correlations between body size and the area, isolation and latitude of islands (see studies summarized in Table 3 of Lomolino, 2005), or equivalently by testing for dynamics in body size following range expansion and vicariance, or tectonic events, climatic fluxes and associated changes in productivity, community structure and isolation of habitats and populations (Case, 1976, 1982, 2002).

    The editorial quickly details some of the current range of hypotheses addressing body size evolution in island contexts, and has a great set of references. I like this paragraph a great deal, it makes many suggestions for research strategies:

    Perhaps most insightful among these new, more integrative research initiatives are the opportunities afforded by the many thousands of introduction 'experiments' performed by human civilizations during their advances across the globe. Each of these episodes of invasion provides an opportunity to investigate how the dynamics in one of the most fundamental characteristics of an organism - its body size - is associated with the dynamics in one of the most fundamental characteristics of a species - its geographical range. A limited, but intriguing number of studies have demonstrated that ecogeographical patterns can evolve in surprisingly short periods of time as an invasive species expands its exotic range and, as a result, experiences repeated founder events and novel selection regimes (Johnston & Selander, 1964; Huey et al., 2000, 2005; Gilchrist et al., 2001; Sax, 2001; Campbell & Echternacht, 2003; Fridley et al., 2006; Patterson et al., 2006). The converse phenomenon - changes in body size and other characteristics of individuals as the species' geographical range contracts - may prove just as insightful. We know that geographical range collapse is far from a random process, with final populations typically persisting in the most isolated reaches of the species' historical range, either along the range periphery, in montane areas or on oceanic islands (Lomolino & Channell, 1995; Channell & Lomolino, 2000a,b; see also Safriel et al., 1994; Towns & Daugherty, 1994; Gaston, 2003; Laliberte & Ripple, 2004). Yet we know of no studies examining the consequences of this highly non-random pattern of range collapse on body-size variation in native or invasive species (Lomolino et al. 2006:1505).

    An integrative perspective on population ecology, adaptations, and displacement in the face of demographic change would certainly improve our understanding of human evolution. In particular, the events of the Late Pleistocene may be explicable only in these terms. But also, taking a broader view of ecological change, ecogeographical changes in Holocene human populations may be examined with this perspective.

    In their list of suggestions, Lomolino and colleagues include this:

    We should capitalize on the thousands of unplanned but well chronicled introduction 'experiments' as opportunities to investigate simultaneously the dynamics of morphological traits and geographical range size. Among these, we include the many waves of invasions and subsequent ecological and evolutionary adaptations of Homo sapiens. Given the available global record on colonization by human civilizations and the substantial morphological variation among individuals and regional populations, ecogeographical studies of our own species may prove especially intriguing (Roberts, 1953, 1978; Ruff, 1994; Bindon & Baker, 1997; Brown et al., 2004; Morwood et al., 2004) (Lomolino et al. 2006:1507).

    Lately, with the exception of Flores, research into hominid body mass has emphasized global patterns rather than regional ones. But the most interesting questions lately have arisen as a result of observing interregional and within-region diversity in body sizes (particularly at the Australopithecus-Homo transition).

    My favorite factoid lately -- you can ask my classes -- is the location of the tallest contemporary human population. The Netherlands.

    References:

    Lomolino MV, Sax DF, Riddle BR, Brown JH. 2006. The island rule and a research agenda for studying ecogeographical patterns. Journal of Biogeography 33:1503-1510. doi:10.1111/j.1365-2699.2006.01593.x

    Tags: 
    Late Pleistocene
    Flores
    allometry

  • Floresiensis presentations

    Tue, 2007-04-03 00:36 -- John Hawks

    I'm at the AAPA meetings in Philadelphia this week, which were preceded yesterday and today by the meetings of the Paleoanthropology Society.

    There were several interesting papers given today, but I wanted to pass along the abstracts of the two pertaining to the Flores hominids:

    "Allometric Scaling of Craniofacial Shape: Implications for the Liang Bua Hominins"

    K. Baab, K. McNulty, and P. Brown

    There has been considerable controversy concerning the taxonomy and evolutionary history of the hominin fossils recovered from the Indonesian island of Flores. One hypothesis is that these individuals were the result of insular dwarfing of H. erectus or a small bodied and as yet unknown hominin from the Asian mainland (e.g., Brown et al., 2004). Alternatively, some have claimed that LB 1 is a microcephalic modern human. This study will take a new approach to investigating the affinities of the Flores hominins by focusing on the three dimensional shape of the LB 1 craniofacial skeleton. To address the possibility of dwarfing in the evolutionary history of the Flores hominins, we also examined allometric scaling of craniofacial shape within the African apes and humans. As a first step, generalized Procrustes analysis was performed and principal components analysis (PCA) was used to explore the shape of the LB 1 neurocranium within a broad range of specimens representing both fossil and extant Homo species using geometric morphometric techniques. PCA indicated that the shape of the neurocranium was aligned most closely with H. erectus. A landmark set which also incorporated facial landmarks again showed similarities with H. erectus, particularly Asian H. erectus, but also with modern humans. The second set of analyses occurred in size-shape space, which, in addition to the Procrustes shape coordinates, also includes the logarithm of centroid size as an additional variable (Mitteroecker, 2004). By performing a PCA in size-shape space, we were also able to explore allometric patterns within and between Gorilla, Pan and Homo. While the apes, modern humans and archaic Homo all have separate trajectories, their slopes are quite similar. The position of LB 1 in size-shape space is compatible with its interpretation as a scaled down version of an archaic Homo species.

    The second paper was much more interesting:

    Morphological affinities of the wrist of Homo floresiensis

    M. Tocheri, W. Jungers, S. Larson, C. Orr, T. Sutikna, Jatmiko, E. Saptomo, R. Due, T. Djubiantono, M. Morwood

    The shape of the trapezoid in Homo sapiens is derived in comparison to the shape in other primates. Whereas the trapezoid of nonhuman primates is shaped like a pyramidal wedge (the narrow tip is palmar while the wide base is dorsal), that of H. sapiens is boot-shaped, resulting from a radio-ulnar and proximo-distal widening of the palmar half of the bone. The human trapezium, scaphoid, capitate, and second metacarpal base exhibit a derived complex of features that correlates with the distinctive shape of the trapezoid. Current paleontological evidence indicates that this derived complex of features evolved as early as 800,000 years ago and is a synapomorphy of H. sapiens and Homo neanderthalensis. The Homo floresiensis type specimen (LB1) includes a trapezoid, scaphoid, and capitate, all well-preserved and non-pathological. These small carpals display none of the aforementioned shared, derived features of H. sapiens and H. neanderthalensis. Rather, these bones are morphologically identical to the conditions seen in all African apes and in Australopithecus afarensis. The trapezoid is wedge-shaped with a small, dorsally-placed facet for the capitate and a large, triangular-shaped facet for the scaphoid, while the capitate and scaphoid exhibit the morphology that is typically correlated with the primitive trapezoid condition. As might be expected, the scaphoid and os centrale of H. floresiensis are completely fused, which is a synapomorphy of Gorilla, Pan, and Homo. The primitive carpal morphology of H. floresiensis is not consistent with hypotheses of a congenital or developmental abnormality afflicting a modern H. sapiens. Rather, the evidence is more consistent with hypotheses that H. floresiensis is descended from a hominin ancestor that migrated out of Africa prior to the evolution of the shared, derived carpal morphology characteristic of H. sapiens and H. neanderthalensis.

    OK, after pasting that and fixing all the markup, I have to say that abstract drops entirely too many taxonomic names. But the basic point of the paper was that the wrist bones associated with the LB 1 skeleton don't look like modern humans. They look like the wrist bones of OH 7, which for these particular bones (trapezoid, scaphoid, and capitate) are similar to chimpanzees and other apes. Tocheri was fairly compelling in the description of the initial shape formation of the wrist bones prior to week 10 of fetal development; any genetic change that affected these shapes would have to be expressed very early. That would tend to make it unlikely that a single developmental change could have caused a modern human to have both the cranial form and the wrist morphology of LB 1.

    There were some missing parts that should be fleshed out -- for instance, how much interpopulational variation is there in these bones in recent humans? The Neandertals overlapped with the modern human distribution, but there was no comparison of means.

    Still, this may be a compelling argument for LB 1 not being modern, assuming the association of the wrist is good.

    In the morning, I'm moderating a session with some more papers about the Flores hominids. I'll report anything interesting (including fights!).

    UPDATE (4/2/2007): Sharp-eyed reader Brian Witte found an html error that spread a case of the italics across the site; many thanks for pointing it out!

    In the last couple of days, I have had correspondence with a number of people about the wrist. Again, I should note that this is an area where a publication will really be required to evaluate the claims; particularly concerning developmental stability as a function of early differentiation.

    Tags: 
    Homo erectus
    A. afarensis
    meetings
    Flores
    Neandertals

  • Hobbit Idol

    Mon, 2007-04-02 16:32 -- John Hawks

    I felt like Ryan Seacrest Thursday morning, introducing papers about LB 1. There's not really anything new to report, but there were a few dust-ups. The audience was standing room only, with the back of the room five ranks deep. The session had a mix of different talks, and a couple of authors had to cancel, which helped me keep things on schedule. We even had an extra ten minutes after Bob Eckhardt's talk for some discussion and questions.

    A number of attendees let me know afterwards how much they enjoyed the session. I don't know whether that's true of all the authors, but I think I saw each of them smile at some point later in the week!

    As for the talks themselves; I don't really want to give a detailed overview. I've seen lots of presentations during my time blogging, and I've never written a review of any of them. Many talks become papers, and the 15-minute format is really not sufficient to give the kinds of supporting details to support a scientific argument fully. It's just not fair to the research to critique it based on less than the published version.

    But the abstracts are public, and there is certainly some interest in the contents of the talks, so I'll give some quick impressions of what was new. I did that earlier with Tocheri's paper about the wrist bones of LB 1.

    Eckhardt and Dean Falk largely talked about details that were published within the last year. Falk presented some additional comparisons involving the microcephalic samples, mainly to argue that the juvenile specimens in that sample did not bias the endocast comparisons.

    Lisa Nevell from GWU read a paper with many interesting allometric comparisons of LB 1 with recent humans and earlier hominids. This was nice work, and I hope to see it come out in publication. Still, the final sentence of the abstract says a lot:

    These results are consistent with the taxonomic validity of Homo floresiensis, although they do not rule out the possibility that LB1 is pathological.

    That ultimately is the bottom line of much work on LB 1, of course. Eckhardt pointed out that hundreds of conditions manifest with microcephaly as a symptom. Distinguishing a rare pathology from a rare pattern of evolution is an inconvenient problem.

    The paper by Susan Larson and colleagues was read by Bill Jungers (Stony Brook). The conclusions of the presentation are summarized in the abstract's last paragraph:

    We have examined the Liang Bua fossil material and find the analyses of the LB1 postcranial material by Richards (2006) and Jacob et al. (2006) to be incorrect on nearly all counts. Contrary to both Richards and Jacob and colleagues, both limb proportions and stature reconstruction for LB1 are completely outside ranges ever observed in modern humans, including the smallest "pygmoids." Previous studies have shown that muscularity cannot be deduced reliably from muscles scars. In addition, Jacob et al. (2006) exaggerate the degree of left/right asymmetry in LB1, and cortical bone thickness is perfectly normal and well within modern ranges.

    It was after this paper that the questions became the most heated, as there are plainly differences in interpretation -- and in primary data -- between Jungers (and coauthors) and Eckhardt (and coauthors). It's really not possible to evaluate these differences fully without access to a published account.

    I imagine that all the attendees probably thought much the same.

    Tags: 
    meetings
    Flores

  • Size, shape, and microcephaly

    Wed, 2007-02-07 09:18 -- John Hawks

    I've been taking quite a lot of notes while studying last week's paper by Dean Falk and colleagues.

    The lede in all the articles about Falk and colleagues' paper is that they show that LB1's endocast is normal. But is it?

    As Ralph Holloway and colleagues (2006) have noted, LB1 is not the same shape as an average-sized human endocast. It has strange protrusions in Brodmann's area 10 of the prefrontal cortex, it is very flat from top to bottom (platycephalic), it has an unusual proportion of cerebellum to neocortex, and it is quite asymmetrical. There seems to be no substantive disagreement about these features. These features do not show that LB1 had any of the spectrum of microcephaly disorders. But they do show that it's abnormal, at least in the context of modern humans.

    In their supplementary material, Falk and colleagues show that the frontal lobes of microcephalics generally have a flattened orbital surface. In other words, they don't project downward into the space between the orbits so much. LB1 does not share this flattening -- it is like normal humans in this anatomy. I think this is an important observation, though it is not entirely clear how diagnostic it is for microcephalics.

    But the main evidence in the paper relates to their use of a discriminant function to classify LB1:

    As shown here, the frontal breadth relative to cerebellar width and lack of cerebellar protrusion of LB1's endocast classify it with 100% probability with normal H. sapiens rather than microcephalics (2516).

    Them's strong words. Like most biological anthropologists, I have some experience with discriminant functions. It can be easy (although certainly not always!) to get highly significant statistical results, when the original samples are small as they are in this study. Small samples by chance exclude much of the variation that makes classification errors apparent.

    So I looked carefully at the details of the discriminant analysis in this paper. I'm not so convinced they've shown the skull is "normal". I think that another way of looking at the same data makes the endocast look even more unusual.

    Falk et al. (2007) do a great job of describing their methodology and include the StatSoft output for the discriminant function in their supplementary materials, as well as figures showing the distribution of each ratio in their samples. So we can make some progress interpreting exactly how the discriminant function came to its result.

    The statistical analysis will require a bit of explanation for many readers. Here is the relevant text from the paper's methods section:

    Discriminant and canonical analyses were used to study shape differences between virtual endocasts of microcephalic humans (n=9) and normal humans (n=10). For these analyses, we used the four ratios that we thought would discriminate between the two groups (2/1, [2Ð 4]/1, 6/5, and 8/6) (Fig. 2). Data were tested for normality with Shapiro-Wilk W tests, and the homogeneity of the variances and covariances was tested with a Box M test. Backward stepwise discriminant analysis was used to select the most powerful discriminators (SI Table 4). For the stepwise procedure, the F to enter was set at 4; F to leave was set at 3; and the tolerance was set at 0.01. Each discriminator plus the combination of the most powerful discriminators was used to classify each case into the group that it most closely resembled. In addition, LB1, the Basuto woman, and a human dwarf (which were not used to develop the discriminant and classification functions) were classified into the two groups. Posterior classification of cases was based on Mahalanobis distances, with a priori probabilities being proportional to group sample sizes. Data analyses were performed with JMP Statistical Software Release 5.0.1.2 and STATISTICA (data analysis software system, Version 7.1; StatSoft, Tulsa, OK). Scatter plots for the four variables that were analyzed are presented in SI Fig. 5. The data were normally distributed (ShapiroÐWilk W test, P >0.05), and the variances and covariances were homogeneous across groups (Box M test, P

    The discriminant function reported in the paper is based on only two of the ratios. The analysis evaluates the correlations among the variables and eliminates those variables that do not contribute significantly to discrimination. In this case, one of each of the pairs of partly redundant variables was removed. That makes sense: almost all their information is already present in the other two ratios.

    That means that if we chose the excluded variables instead of the ones the function included, we would do almost as well in distinguishing normal from microcephalic. The plots make that very clear -- choose relative cerebellar width and relative posterior base length for the function, and it will still assign the normal and microcephalic endocasts correctly. It just doesn't make very much difference. The reason why cerebellar protrusion and relative frontal breadth were included instead of the other two is that they explain a slightly greater amount of the between-group variance. In other words, they might make a difference if we tried to classify 200 skulls with the same means and variances instead of 20.

    Nor does it make much difference to the classification of LB1. Both the relative cerebellar width and the relative frontal breadth (both partially redundant) would place LB1 with the normal group. In fact, it is beyond the normal group for relative cerebellar width, and beyond the normal mean for relative frontal breadth.

    Wait a second. These two ratios are only different because frontal breadth is substituted for maximum endocast breadth. Yet the placement of LB1 relative to the normal group is highly extreme for one and less extreme for the other (frontal breadth). From this, we can infer (even if we can't see a scatterplot) that LB1 has a relatively narrow frontal lobe compared to its maximum breadth. Falk et al. (p. 2516) wrote as much, noting that the LB1 frontal breadth compared to its maximum breadth was similar to Homo erectus. But "similar to Homo erectus" also means "similar to microcephalics.

    What we have here (judging from the ratios) is an endocast that looks like modern microcephalics. It's cerebellum protrudes posteriorly like a microcephalic. It has a narrow frontal lobe like a microcephalic. It has a relatively short frontal lobe like a microcephalic. There's only one exception: it has a narrow cerebellum.

    What to call a abnormally normal abnormal skull

    Let's review: it is very easy to discriminate microcephalic and normal skulls by size. Every measure or ratio that distinguishes microcephalic and normal skulls will necessarily be related to size, because size defines the groups. A small set of four ratios led to a discriminant function that could classify normal and microcephalic skulls. This discriminant classifies LB1 as "normal". All of the ratios involve the size of the cerebellum.

    I think the observation here is that LB1 is abnormal for its size. Its cerebellum is relatively narrow (compared to brain width) but slightly elongated. This change in shape is what the ratios capture.

    Why should the shape of the cerebellum be unusual in LB1? One explanation is that it isn't -- instead the shape of the neocortex is unusual. In particular, the neocortex is unusually flattened (Holloway et al. 2006). This means that for its small volume, the cerebral breadth is relatively broader, making the cerebellar breadth appear to be relatively short.

    Another explanation is that the developmental alteration leading to small brain size in LB1 occurred in a pathway that affected cerebellar size more than is typical for microcephalics. It is not impossible that this alteration was favored by selection in a population of humans on Flores, but the current evidence cannot demonstrate this. We can just as easily propose that the developmental alteration was a distinctive form of microcephaly not fully captured by the present sample. However, the close similarity of LB1 to microcephalics in most measures hardly weighs against the hypothesis that its brain size was simply pathological.

    In other words, LB1 is abnormally small, abnormally shaped, and abnormal in comparison with other human endocasts of comparably small size. Can this combination of measurements mean that the endocast really is normal after all? I don't think that a triple negative makes a positive.

    Unfortunately, none of these considerations really address the core question, which is whether LB1 had a brain size representative of its population. In fact, I don't think there is any way to answer that question without finding more skulls, because LB1 does show clear evidence of pathology.

    References:

    Bush EC, Allman JM. 2004. The scaling of frontal cortex in primates and carnivores. Proc Nat Acad Sci USA 101:3962-3966. doi:0.1073/pnas.0305760101

    Falk D, Hildebolt C, Smith K, Morwood MJ, Sutikna T, Jatmiko, Saptoro EW, Imhof H, Seidler H, Prior F. 2007. Brain shape in human microcephalics and Homo floresiensis. Proc Nat Acad Sci USA 104:2513-2518. doi:10.1073/pnas.0609185104

    Holloway RL, Brown P, Schoenemann PT, Monge J. 2006. The brain endocast of Homo floresiensis: microcephaly and other issues. Am J Phys Anthropol 129 (supplement):105.

    T. Jacob, E. Indriati, R. P. Soejono, K. Hsü, D. W. Frayer, R. B. Eckhardt, A. J. Kuperavage, A. Thorne, and M. Henneberg. 2006. Pygmoid Australomelanesian Homo sapiens skeletal remains from Liang Bua, Flores: Population affinities and pathological abnormalities. Proc Nat Acad Sci USA. PNAS published August 23, 2006, 10.1073/pnas.0605563103

    Martin RD, MacLarnon AM, Phillips JL, Dobyns WB. 2006. Flores hominid: new species or microcephalic dwarf? Anat Rec 288A:1123-1145. doi:10.1002/ar.a.20389

    Tags: 
    Flores
    Homo erectus

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