john hawks weblog

paleoanthropology, genetics and evolution

Homo erectus

  • The Denisova genome FAQ

    Wed, 2010-12-22 12:35 -- John Hawks

    Today, a paper by David Reich and colleagues presents the nuclear genome of the Denisova pinky bone [1]. This is the second “whole genome” of an apparently extinct population of Pleistocene humans. This genome is nearly as distinct from Neanderthals as the draft Neanderthal genome is from living people.

    Between the draft Denisova genome, the draft Neanderthal genome, and the genomes of living people, we now have a record of three human populations that share origins relatively early in the Pleistocene.The paper presents some population modeling that attempts to estimate the divergence times and levels of gene flow among these populations. I think as a first effort these models answer some questions definitively, but leave substantial room for elaboration and improvement. There are many clear mysteries, most notably whether any known fossil samples can be attributed to the population represented by the Denisova sequence.

    The most significant finding in the paper is the demonstration that some living humans trace significant fraction of their ancestry to the population represented by the Denisova genome. As in the case of Neanderthals, different human populations show significantly different levels of similarity to the Denisova sequence. For Neanderthals, the similarities indicated between one and four percent Neanderthal ancestry for living people outside of Africa. In the case of the Denisova sequence, the greatest similarities are with living people in Melanesia – in this paper, represented by genome samples from Papua New Guinea and Bougainville. The similarities are consistent with approximately 4% contribution of a Denisova-like population to the ancestry of these living Melanesians.

    The paper estimates that together, the Denisova and Neanderthal-derived genes account for 8% of the ancestry of these living people.

    I find that estimate stunning, it's a huge contribution into living populations by these ancient Pleistocene populations.

    The paper additionally reports the mtDNA of a second individual from Denisova Cave, represented by an isolated third molar. This mitochondrial sequence is very similar to the sequence of the pinky bone, which I count as very important because it means there is potentially a population here. However, they do not report any nuclear genome results from this second individual.

    Those are the basic headline results. As I often do, I've prepared a series of frequently asked questions about the paper. This one is very dense with information content, and that includes 90 pages of supplementary information. We'll be working through it carefully during the next few weeks. The most exciting part is that, like the Neanderthal genome, these data will be available for other researchers to study. My lab has been intensively going through the Neanderthal genome with several hypotheses in mind, and we are eager to start working with the Denisova sequence.

    Could we have predicted this result?

    There were pretty clear hints that something interesting may have been going on with the population structure in the ancestry of living people in Papua New Guinea. My graduate student, Aaron Sams, has been looking into the hypothesis of a deeper Pleistocene component of ancestry in this population for the last few months. Of course we had earlier this year the announcement from Keith Hunley and Jeff Long's group that microsatellite variation was consistent with an ancient Pleistocene structure to the ancestry of Melanesians.

    Our notion here was that we could use ascertainment bias within the public sets of SNP data to look for deeper genealogical roots within some populations. Because most single nucleotide polymorphisms have been ascertained in Europeans, and secondarily within other populations represented in biomedical contexts or the HapMap – chiefly Africans and East Asians – there is a chance that a deep genealogical root in Melanesians might be obviously represented by a haplotype bearing all ancestral polymorphisms. That's not to say that the population is more ancestral than other populations, just that the unique derived variants in that population were not ascertained.

    By targeting these regions with all-ancestral haplotypes, we began to make substantial progress identifying regions as candidates for a more ancient population structure in this part of the world. Pretty exciting stuff in the absence of an ancient human genome. But now the Denisova sequence gives us a very clear sign that such regions should be very widespread across the genome. Some of them are presently at high frequencies within samples of PNG genetic variation, so there is a good chance that some variants will turn out to be of adaptive importance in this population.

    The point is, this result doesn't come from nowhere. It was clearly anticipated by analysis of the genetic variation within living Melanesians. It is perhaps a bit of a surprise that an ancient genome from southern Siberia would provide so many genealogical ties to this island population. That will require us to give some close consideration to the population structure of Pleistocene people as well as the migration history leading to the peopling of Oceania.

    What is this tooth?

    The paper identifies the tooth as an upper third molar, or possibly as a second molar. What we can say about it is that it's relatively large. In fact its length and breadth put it within a size range occupied by australopithecines and early Homo, both H. habilis and H. erectus. There are no distinctive morphological characters that would allow it to be assigned to any taxon.

    What the paper doesn't point out is that there are Upper Paleolithic specimens that equal or exceed this tooth in size. For example, the measured length and breadth of an upper second molar from Oase, Romania, are larger than this specimen, and the third molar (in the crypt) of that specimen is yet larger. There is an Upper Paleolithic-associated molar from Turkey which is also exceedingly large.

    I don't take that as a sign of relationship between this specimen and early Upper Paleolithic people -- even though these are some of the earliest. It is another sign of how non-diagnostic this tooth actually is. I would say that in the absence of genetic information, we'd be looking at these remains as likely early Upper Paleolithic people, and accentuating these similarities.

    With the genome, there's a tendency to assume a completely opposite attitude -- that they must represent something separate and different from Upper Paleolithic people. That may be an overreaction -- the evidence of gene flow suggests the possibility of continued interaction among these Late Pleistocene groups.

    What happened to the X-Woman?

    I guess when they found a second individual, it was better to have a name for the group rather than the individual. Or maybe somebody didn't like the name X-Woman. As in, "I wonder what happened to the Oneders".

    Anyway, the paper uses the term "Denisovans" for this ancient population. That implies a certain agnosticism about whether any particular kinds of fossil humans might belong to the same population as the two sequenced individuals.

    How were the Denisovans related to Neandertals?

    Remembering that the Neandertal draft genome contains a very high fraction of spurious unique changes, Reich and colleagues performed a similar series of statistical comparisons to those done by Green and colleagues in the Neandertal analysis. Most prominent is limiting the comparison to places where humans and chimpanzees are known to differ. By targeting these sites, the analysis cuts the rate of false positive changes to a manageable level.

    I mention that because it is necessary to make sense of the direct quotes:

    The Denisova genome diverged from the reference human genome 11.7% (CI: 11.4–12.0%) of the way back along the lineage to the human– chimpanzee ancestor. For the Vindija Neanderthal, the divergence is 12.2% (CI: 11.9–12.5%). Thus, whereas the divergence of the Denisova mtDNA to present-day human mtDNAs is about twice as deep as that of Neanderthal mtDNA, the average divergence of the Denisova nuclear genome from present-day humans is similar to that of Neanderthals.

    So the Denisova, Neandertal and human genomes are close to a trichotomy in terms of their average relationship. For any particular gene, of course, there may be sister pairings between any two of those three -- and in many cases, between Denisovans and some living humans to the exclusion of other living humans. This gives rise to several tricky statistical issues as we consider particular gene loci.

    For the moment, we'll consider the genome-wide average. How similar are Denisovans and Neandertals? Reich and colleagues considered the subset of sites where two sequences (out of Denisova, Neandertal and human) share a derived SNP variant:

    The number of sites where the Denisova individual and Neanderthal cluster to the exclusion of the Yoruba and chimpanzee is 46,362, compared with an average of 22,012 sites for the other two possible patterns (Yoruba and Denisova, or Yoruba and Neanderthal). This excess of sites where Denisova and Neanderthal cluster supports the view that the Denisova individual and Neanderthals share a common history since separating from the ancestors of modern humans (Supplementary Information section 6).

    They share twice the number of derived variants compared to the human in their comparison. Denisovans and Neandertals shared substantial ancestry with each other. That may mean they emerged from a single population -- possibly the early Middle Pleistocene population of Eurasia. Or it may mean that they exchanged genes after they reached Eurasia.

    Reich and colleagues address this issue further by comparing pieces of two Neandertal genomes with Denisova. The Mezmaiskaya specimen is represented by much less sequence than the Vindija draft genome but it is geographically intermediate between Croatia and Denisova. By including this specimen with the Neandertals, Reich and colleagues could do a statistical analogue of FST -- giving a way of examining the extent of genetic exchanges between the ancestors fo these Neandertals and Denisovans. They found that the Mezmaiskaya and Vindija specimens were much more likely to share alleles with each other than with the Denisova sequence. It's a striking statistic -- if you do the same comparison with living people, they're 10 percent or so more likely to share alleles with neighbors than with distant individuals; Neandertals were apparently 65 percent percent more likely to share alleles with each other than with Denisova. It's not an exact stand-in for FST, but it's nearby. This was a highly structured Pleistocene population.

    Is the nuclear variation consistent with the mtDNA?

    I wrote about the Denisova mtDNA sequence last spring ("The Denisova mtDNA sequence: The X-Woman"). The sequence is an outgroup to a clade including both humans and Neandertals, and appeared to branch from our ancestors roughly a million years ago. That appeared to be a very interesting date -- possibly consistent with Homo erectus, but too recent to reflect the first dispersal of Homo from Africa, more than 1.8 million years ago.

    That mtDNA divergence date was not easily interpreted. As I pointed out at the time, it might have been consistent with incomplete lineage sorting in a single widespread human population -- maybe even the Neandertal population.

    Reich and colleagues show that the mtDNA divergence between Denisova and the modern-Neandertal clade is deeper than expected given the nuclear genome genealogical divergence. They also show that the nuclear genomes of Neandertals and Denisovans are somewhat closer than either is to the majority ancestors of living people. They discuss two possible explanations.

    One scenario a mixture of the Denisovans with a more ancient Pleistocene population, followed by introgression of a more ancient mtDNA clade into the Denisovans. This would assert an ancient structured population preceding the origin of Denisovans, presumably from one of the Middle Pleistocene populations of Africa or Eurasia.

    A second scenario is incomplete lineage sorting, in which an earlier mtDNA divergence was captured by the Denisova and Neandertal populations at the time of their divergence and differentially lost from them.

    Reich and colleagues show that both these scenarios may be consistent with evolution by genetic drift in these ancient groups, given some assumptions about their population sizes.

    I think there are still some reasonable questions about the relative dates of divergence, but those can probably be answered by considering the full pattern of variation of genealogies across the genome. Additionally, there may be uncertainty about the mutation rates used in both the mtDNA and nuclear comparisons. That's one reason why I consider the population models here to be a first draft of the real history.

    What are the archaeological associations?

    The current paper is more clear about the site's dating and stratigraphy than the earlier, shorter paper by Krause and colleagues [2]. In the spring, it appeared that the pinky bone was associated with the Upper Paleolithic at the site. In the current paper, the authors explain the complexity of layer 11, which contains both Upper Paleolithic industry and these skeletal and dental remains:

    The small size of both the phalanx and the tooth precludes direct radiocarbon dating. We instead dated seven bone fragments found close to the hominin remains in layer 11 in the east and south galleries. To ensure that they were associated with human occupation of the cave we chose bones that have evidence of human modification, including a rib with regular incisions and a bone projectile point blank generally associated with Upper Palaeolithic cultural assemblages. In the south gallery, where modified bones were not available, we used herbivore bones (Supplementary Information section 12).

    Four of the seven dates are infinite dates older than 50,000 years BP (uncalibrated), whereas three are finite dates between 16,000 and 30,000 years BP (Supplementary Table 12.1). The rib with incisions and the projectile point blank are about 30,000 and 23,000 years BP, respectively. Together with three previous dates23 this shows that layer 11 contains cultural remains from at least two different time periods, one period older than 50,000 years BP and one more recent period. However, the stratigraphy is complicated by the discovery of a wedge- shaped area close to the area where the phalanx was found that is likely to be disturbed (Supplementary Information section 12). Hominin remains large enough to allow direct radiocarbon dates may even- tually be discovered in the cave, but a reasonable hypothesis is that the phalanx and molar belong to the older occupation.

    So, no direct dates. By inference (of their weird-looking genetic sequences), the two skeletal individuals are likely to be older than the Upper Paleolithic, but the stratigraphy does not require this. There is a mixing of older and younger materials.

    Adding to the problem, the finger bone has anomalously good preservation of DNA -- the authors point out in the first paragraph of the discussion:

    The molecular preservation of the Denisova phalanx is exceptional in that the fraction of endogenous relative to microbial DNA is about 70%. By contrast, in all Neanderthal remains studied so far the relative abundance of endogenous DNA is below 5%, and typically below 1%. Furthermore, the average length of hominin DNA fragments in the Denisova phalanx is 58 base pairs (bp) (SL3003) and 74 bp (SL3004) in spite of the enzymatic treatment that removes uracil residues and decreases the average fragment size, whereas in most well-preserved Neanderthal samples it is 50 bp or smaller without this treatment. Thus, although many Neanderthals are preserved under conditions apparently similar to those in Denisova Cave, the Denisova phalanx is one of few bones found in temperate conditions that are as well preserved as many permafrost remains. It is not clear why this is.

    They can rule out some explanations because the molar does not have the same exceptional preservation. At the moment, we can probably just chalk it up to good luck. But I think the issue is not irrelevant to the problem of dating. What is going on with this site? Very unusual.

    Why Melanesians?

    Denisova Cave is in southern Siberia. The hominin occupation of the cave appears to have been within the last 50,000 years. People reached Sahul sometime before 40,000 years ago. How in the world did these people come into contact?

    The most plausible hypothesis is that the Denisovans represent a much larger and more widespread population across South and Southeast Asia. A population dispersing in the direction of island Southeast Asia would have encountered and mixed with this population. The dispersing population would have absorbed some adaptive genes, which would have increased in frequency thereby increasing the apparent genetic contribution of the indigenous Pleistocene population.

    This leaves some unanswered questions.

    1. Who were these ancient people? Were they "Homo erectus"?

    This would be my null hypothesis -- that we are looking at one site representing a widespread population across the eastern extent of Eurasia, including Sundaland, during the Middle Pleistocene. However, this scenario is not fully consistent with the population model presented by Reich and colleagues. In particular, they derive Denisovans and Neandertals from a single ancestral population that diverged from humans sometime during the last 500,000 years. That means that the type specimen of Homo erectus (roughly a million years old) cannot possibly have been part of the Denisovan population. Most of the fossil record of Homo erectus in Asia is too old to have been part of a Denisovan population.

    2. Why do the other populations of East and Southeast Asia not show clear signs of mixture with the Denisovans?

    The statistics in the paper show a clear (and large) component of Denisovan ancestry in the PNG and Bougainville genomes, but no large component elsewhere in Asia. Reich and colleagues address this question briefly.

    An interesting question is how widespread Denisovans were. A possibility is that they lived in large parts of East Asia at the time when Neanderthals were present in Europe and western Asia. One observation compatible with this possibility is that Denisovan relatives seem to have contributed genes to present-day Melanesians but not to present-day populations which currently live much closer to the Altai region such as Han Chinese or Mongolians (Table 1). Thus, they have at least at some point been present in an area where they interacted with the ancestors of Melanesians and this was presumably not in southern Siberia.

    Probably the best explanation for the disproportionate impact of the gene flow into the ancestors of Melanesians is a kind of peninsula effect -- they encountered these people early, moved along through their population the furthest, and acquired a substantial signature by a combination of selection and "surfing" neutral alleles along with population expansion. We can assume, I think, that Melanesians are not unique. We do not have a substantial genetic representation of island Indonesia or Australia in these comparisons, I would expect they trend in the same direction. Also, Melanesian-derived genes make up a large component (upwards of 20 percent) of the nuclear genome of Polynesians today. This is a large population of people with Denisovan genes, in other words.

    But why not China? Why not South Asia? These are extremely interesting questions. Were the Denisovans not present in China -- was there possibly yet another Pleistocene population there?

    Why not call them "Homo erectus"?

    Formally, we don't know whether the individuals represented by these genetic samples would have had the diagnostic features of Homo erectus. They don't live especially near the main samples of Homo erectus, and they lived long after the main samples of Homo erectus appear to have existed.

    But worse, as I indicated above, there are serious inconsistencies between the fossil record and the population model presented by Reich and colleagues.

    1. "Homo erectus", as usually understood, occurred widely in Asia, including China and Java, and Africa during the span from 1.95 million to 750,000 years ago. In China and Java, fossils attributed to Homo erectus persisted until 200,000 years ago. There is no unequivocal fossil of Homo erectus after 200,000 years ago (including some not-yet-published redating). I'm obviously glossing many complexities in that description, but trying to pose the species in the broadest possible geographic and temporal range.

    2. Green and colleagues [3] derived Neandertals from a common ancestor with living Africans only 250,000-400,000 years ago. A model including the Denisova data is provided in the current paper. It has wider confidence limits and reports the answers in generations. If we assume 20-year generations, the current paper puts the emergence of a Neandertal-Denisova clade at between 190,000 and 520,000 years ago, and the divergence of the Neandertal and Denisova branches around 50,000-100,000 years later.

    In other words, possibly sometime after the time of the last unequivocal H. erectus fossils, the Denisovan population was diverging from Neandertals. These events occurred more than a half million years after the Trinil individual -- type specimen of Homo erectus -- lived.

    3. Millions of living people have their ancestry in these Pleistocene populations. That tends to make their identification as different species somewhat problematic. Even if we could identify the Denisovan population with the fossil evidence of Homo erectus, maybe they don't merit that species-level distinction. Or maybe we should recognize two or more distinct populations within what we now call Homo erectus.

    And before you splitters out there get excited -- these would not be the same two populations (H. ergaster and H. erectus) currently promoted by some paleoanthropologists. That issue is way too early to be consequential in the current context.

    Some of these issues can be solved by altering the population model. For example, if we assume a slower mutation rate (consistent with comparisons between parents and offspring in living people), the estimated divergence times will be much higher, possibly consistent with a widespread population at the time of Zhoukoudian or Sangiran. It's not obvious that this would fully bring the genetics into accord with the fossil record, but it would eliminate many inconsistencies.

    What drives you crazy about this?

    Well, it's obviously very exciting, but I find it very difficult to talk about these Pleistocene populations without falling into bad habits.

    Our common ancestry as humans goes back to the Early and Middle Pleistocene. The (now multiple) Neandertal genomes and the Denisova genome share genes with some people and not others because of this common ancestry.

    In addition, some living people carry even more genes from Neandertals because they have an appreciable fraction of Neandertal ancestry. That makes it nonsensical to talk about "Neandertals and the ancestors of modern humans". Neandertals are among the ancestors of modern humans.

    Just so with Denisova. It's nonsensical to talk about a three-way split between Neandertals, Denisova and modern humans. We can talk about a population model with a clade separating an ancestral Neandertal-Denisova population from contemporary Africans.

    I have to remind myself again and again when I talk to people about these issues that "modern human ancestors" is not a group that excludes these Pleistocene people.

    Once we put ourselves into the mode where we are referring to a population model, it is important to recognize the limitations of those models. For example, we cannot presently exclude many kinds of gene flow among these Pleistocene populations. We can understand some limits to the level of gene flow -- these populations were highly structured, it wasn't Pleistocene panmixia. But it is premature to talk about isolation without recognizing the limits of our ability to test these population models.

    The difficulty with terminology tells us something very important. A large-scale reorganization of the science of human origins is upon us. The terms we are used to using will, many of them, become obsolete. Some now-obscure terms will become very important.

    We might think the new terms are likely to be technological -- but I think that the technology is changing too fast for that. Most people won't need to learn the ins and outs of a particular sequencing platform, because in two years it will be obsolete.

    No, much more important is our way of talking about the relations of biological and cultural evidence. What does an archaeological pattern mean, and how does it relate to biological connections between populations? How can we identify the genetic causes of skeletal and dental phenotypes? What is the importance of a morphological or phylogenetic species in the context of these clear signs of genetic intermixture?

    Many of these are old questions. They are about to get new answers, addressed in a new way using new evidence.

    References

    1. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature [Internet]. 2010;468:1053–1060. Available from: http://dx.doi.org/10.1038/nature09710
    2. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Paabo S. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature [Internet]. 2010;464:894–897. Available from: http://dx.doi.org/10.1038/nature08976
    3. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, et al. A Draft Sequence of the Neandertal Genome. Science [Internet]. 2010;328:710–722. Available from: http://dx.doi.org/10.1126/science.1188021
    Tags: 
    Homo erectus
    Melanesia
    Neandertals
    population structure
    Denisova
    introgression
    Neandertal DNA
    out-of-Africa
    Synopsis: 
    A genome from the Altai is revealed as a representative of an ancient hominin population new to science.

  • The shrinking youth

    Fri, 2010-09-17 13:59 -- John Hawks

    Yesterday the Journal of Human Evolution released a new paper by Rhonda Graves and colleagues, titled “Just how strapping was KNM–WT 15000?” [1]. The paper challenges almost 25-year-old estimates for the body size of this important 1.5 million year old skeleton.

    For all this time, the textbooks have reported that early Homo in Africa had the same tall and elongated physique as current East African people like the Maasai. The new paper says that the textbooks are wrong -- the skeleton doesn't represent an individual who would have grown to be 6'1" (185 cm), instead it was near the end of its growth trajectory, for an adult height of around 5'4" (163 cm).

    That's a pretty massive change, and when the authors presented this work at the AAPA meetings last spring, it wasn't without controversy. So naturally we should look closely at the paper, understand its conclusions, and assess what this new estimate means for our understanding of early Homo. As you might guess from reading some of my earlier posts, I've been thinking that the body sizes of the rest of the Pleistocene record add up to a fairly simple picture. One of the few outliers from this picture was KNM-WT 15000. I'm inclined to think that the new estimate fits the bigger picture -- for example, I wrote this spring about "Shrinking erectus".

    Which means, of course, that I should be even more skeptical.

    KNM-WT 15000 was a juvenile at the time of death, and so any estimate of body size involves some assessment of the skeleton's state of development. This has presented a problem for assessing how much the individual had still to grow at the time of its death. The eruption and development of the teeth appear to be consistent with a fairly young age at death, by most estimates younger than 11 years, and by some as young as eight. That's using a human frame of reference. If we turn to a frame of reference drawn from chimpanzees or other apes, the estimated age at death from tooth development is even a bit younger. In contrast, the state of bone development seems to indicate a somewhat higher age at death: older than 11, and by some estimates as old as 15 years.

    KNM-WT 15000 skeleton

    Graves and colleagues, looking at this apparent mismatch between dental and skeletal development in this specimen, suggests that we need to look at a broader range of possible developmental models for early Homo erectus. A modern human developmental model is not a good fit, and neither is an ape developmental model. So their study involves creating a range of possible developmental trajectories for early Homo. These trajectories are based on data from living apes and humans, but altered by accelerating some phases or changing the intensity of the adolescent growth spurt.

    The growth spurt is very important to this issue, because it's one way that humans and most other primates differ greatly. Growth during that phase of development contributes disproportionately to the tall stature of modern humans. If Homo erectus didn't have the same kind of growth spurt as we do, then the stature of this specimen would have been a lot shorter than we would estimate for a human of the same age.

    The section of Graves and colleagues' discussion that covers the adolescent growth spurt is, to my mind, the central issue in the paper. Their review begins with a survey of literature on why a growth spurt exists. Most assume that there is some kind of trade-off between early weaning in humans, brain growth, and a large adult body size–with the optimal solution being slow juvenile somatic growth, fast juvenile brain growth, and they “catch up” of somatic growth during adolescence. Graves and colleagues assert that this pattern was not present in early Homo erectus, and that a more chimpanzee like growth spurt may be a better model.

    The velocity growth curves for human stature and chimpanzee total body length (summed length of crown-rump, femur, and tibia) highlight the difference between modern human and chimpanzee growth and development (Fig. 1). Both species exhibit growth spurts, but these spurts differ in rate, timing, and duration (Leigh, 1996). Pre-pubertal growth spurts in mass have been documented in many primates ([Tanner, 1962], [Laird, 1967], [Timiras and Valcana, 1972], [Leigh, 1996], [Leigh and Shea, 1996] and [Hamada et al., 1996]), but to date only slight increases in crown-rump length and total body length have been observed in chimpanzees (Hamada and Udono, 2002). Male chimpanzees (and possibly macaques) undergo a small growth spurt in length during the period between emergence of the first and third molars ([Watts and Gavan, 1982] and [Tanner et al., 1990]), but peak velocity is not as high and the growth spurt not as extended as in modern human adolescence. The velocity of chimpanzee growth decreases slightly between the ages of four and eight, and then begins to decline rapidly until adult total body length is reached at between 12 and 13 years of age. Chimpanzee growth spurts therefore differ in their onset, offset, and intensity compared to the modern human adolescent growth spurt (see Fig. 1; [Bogin, 1993] and [Bogin, 1996]). The growth spurts in the “ALH 12.3/25%” and “ALH 12.3/50%” curves approximate the juvenile pre-pubertal growth spurt exhibited by chimpanzees, which is of shorter duration and lesser magnitude than the full-blown modern human adolescent growth spurt. We contend that these curves most closely match what is currently known about growth and development in H. erectus but acknowledge that the data currently available limit our ability to choose a single curve. It is also possible that future studies documenting growth in wild chimpanzee length may provide evidence to support a different set of growth curves.

    Their small stature estimate for KNM-WT 15000 doesn't entirely hang on this point, but this assumption about the growth spurt makes more difference than any other single factor.

    We can reasonably ask: is there any other support for this assumption?

    The apparent mismatch between dental and skeletal developmental patterns in the specimen is consistent with the lack of a humanlike growth spurt. But evidence from the skeleton itself is weakened by the fact that KNM-WT 15000 appears to have suffered from some kind of growth pathology, as argued by Latimer and Ohman [2]. The pathology argument has mostly come into play over the issue of vertebral canal size in the specimen, but anything that affected skeletal growth may well have affected the relation between epiphyseal closure and dental eruption. Naturally, if the developmental pathology was a significant influence on growth, then we shouldn't be using WT 15000 as a model for early Homo erectus stature anyway.

    A more relevant argument is that KNM-WT 15000 is really an outlier when we assume that it would have grown to a very tall stature. On first appearance, this seems correct. We have quite a number of femora from Homo erectus, both inside and outside of Africa. Only two of them approach the length that had been estimated for the Nariokotome adult stature estimate. KNM-WT 15000's former adult estimate is the extreme.

    But looking more closely, both those tall individuals come from generally the same time and place as KNM-WT 15000. KNM-ER 1808 and KNM-ER 736 both preserve partial femur shafts with estimated lengths above 480 mm. Both specimens are a bit older than Nariokotome, between 1.6 and 1.7 million years old. KNM-ER 1808 in particular contributed heavily to the argument that early Homo erectus had a very tall stature, because the partial skeleton includes a fragment of pelvis, argued to be female. A tall woman makes for a very tall species.

    Still, these two specimens don't seem as significant in 2010 as they did twenty years ago. The Gona pelvis suggests that we don't really know the sex of KNM–ER 1808. Its pelvic fragment looks female in the context of living human dimorphism, but quite possibly male compared to the Gona individual. Henry McHenry [3] estimated adult statures for the KNM–ER 1808 and KNM–PR 736 femurs, both around 5'10" (180 cm). Those are the tall end of stature estimates for Homo erectus, both taller than average for living humans. But perhaps neither is surprising when taken as the largest and of the distribution that on the whole is relatively small bodied. An estimate of 163 cm for the adult height of KNM-WT 15000, as suggested by Graves and colleagues, would not be an outlier in this population, but neither would an estimate as large as 180 cm.

    So I think the comparative evidence is equivocal. Revisiting the specimen with a smaller estimate is reasonable, but I think our ability to assess the accuracy of any estimate is very limited. In light of the pathology of KNM-WT 15000, it may not be very relevant to understanding body size evolution in early Homo, anyway.

    The main problem facing us with understanding body size in early Homo is deciding which specimens should be included in which taxa. If we exclude everything except the relatively tall ones, like KNM–ER 1808 and KNM–ER 736, then we are going to end up with a tall stature estimate for a population, putatively H. erectus. But if we include some of the smaller specimens, like KNM–ER 993, or KNM–ER 803 – both contemporaries of the Nariokotome skeleton – than the average for this more inclusive population will be a lot lower. In East Africa 1.5 million years ago we can't assign an isolated femur to a species, and we won't have a good answer for this issue until we have many more associated specimens.

    I tend to think that small stature is the null hypothesis now, given our knowledge of the small stature of the Dmanisi hominins, and the moderate body size of middle Pleistocene Homo everywhere else. There are a few specimens that represent individuals as tall as those indicated by KNM-ER 736 and KNM-ER 1808, but none taller, and many much shorter.

    It's a much deeper topic than one skeleton, but the problems assessing stature in that skeleton help to highlight the difficulty of the problem in a global sense.

    UPDATE (2010-09-18): A reader suggests that I give a link to a 2004 paper by Shelley Smith, which compared the dental and skeletal maturation of KNM-WT 15000 to a large growth series of modern Canadians [4]. She found cases in the sample with comparable mismatches of dental and epiphyseal age estimates, and argued that we can't exclude a humanlike growth spurt for early Homo. That's one reason why I think this issue can't be resolved -- the variation in humans is great enough to encompass the known fossil specimens.

    A similar lack of resolution applies to enamel growth increments in KNM-WT 15000 ("Dental growth in early Homo"). The specimen can't be distinguished from Australopithecus, but the range in modern humans is very extensive.

    At the moment, skeletal correlates of growth don't give us the resolution to answer these questions definitively about early Homo. If we had more specimens, we could at least reduce the component of error from sampling, which would help considerably. But we can't expect that anytime soon.

    References

    1. Graves RR, Lupo AC, McCarthy RC, Wescott DJ, Cunningham DL. Just how strapping was KNM-WT 15000?. Journal of Human Evolution. 2010;59(5):542 - 554.
    2. Latimer BM, Ohman JC. Axial Dysplasia in Homo erectus. Journal of Human Evolution. 2001;40:A12.
    3. McHenry HM. Femoral lengths and stature in Plio-Pleistocene hominids. American Journal of Physical Anthropology. 1991;85:149–158.
    4. Smith SL. Skeletal age, dental age, and the maturation of KNM-WT 15000. Am. J. Phys. Anthropol. [Internet]. 2004;125:105–120. Available from: http://dx.doi.org/10.1002/ajpa.10376
    Tags: 
    body size
    Homo erectus
    Nariokotome
    Africa
    Early Pleistocene
    Kenya
    stature
    Synopsis: 
    The Nariokotome skeleton once defined the tall linear body form for early Homo. Now it's 5'4".

  • Ngandong interview

    Fri, 2010-07-30 10:58 -- John Hawks

    Nature News has run a nice interview with Russell Ciochon about the new excavations at Ngandong, Java.

    We've been excavating for 24 days without a break. The days blur together and we often lose track of time. There is a routine to systematic palaeoanthropological excavation: opening an excavation pit, digging down to the bone bed, carefully mapping the strata as we proceed, exposing the fossils, assigning the fossil a number, charting its xyz coordinates, removing the fossil, and then sampling the strata for geological analysis and dating.

    Tags: 
    Java
    Homo erectus
    Ngandong
    Asia

  • Shrinking erectus

    Tue, 2010-04-27 10:02 -- John Hawks

    Ann Gibbons reports on the AAPA meetings with a story about all the Homo erectus pelvis and stature papers ("Human ancestor caught in the midst of a makeover," subscription required). Research on the proportions of early Homo was the main event of the meetings, and Gibbons really caught the highlights of the story.

    I wrote about body size in Homo erectus a few months ago, and much of the story follows from the basics I outlined there ("The changing height of Homo erectus"). But there I emphasized that the estimated adult height of KNM-WT 15000 was an outlier in a relatively small body size distribution.

    What I didn't anticipate is that some interesting work might come along to question the tall adult stature estimate for that skeleton. Gibbons describes the work of Ronda Graves and colleagues, presented at the meetings:

    Using intermediate growth rates, graduate student Ronda Graves of Stony Brook University in New York state calculated that Nariokotome Boy would have had less time than originally predicted to reach his adult height when he died. She estimated at the meeting that he would have reached 163 cm in height and 56 kg in weight as an adult—"shorter and wider" than previously thought.

    This seems very short, at least when I first saw it. On reflection, Ohman and colleagues (2002) had provided a stature estimate at death of KNM-WT 15000, as only 147 cm, and they suggested it might have been as short as 141 cm. That's an awful lot shorter than had previously been estimated on the basis of regressions.

    If Graves and colleagues are right about the lack of a human-like growth spurt, an additional 20 cm (8 inches) wouldn't be unusually small for an adult stature. Those stature estimates would put KNM-WT 15000 between the 50th and 90th percentiles for American 10-year-old boys, or between the 25th and 75th percentiles for 11-year-olds. By contrast, an adult stature of 163 would be around the 3rd percentile for adult American men. The assumptions about growth totally determine the outcome for adult height.

    The credibility of the growth assumptions can only be tested by looking at other adult and juvenile remains. There is much more to say on this topic, but I'll point out one relevant comparison: The estimated stature of the adult skeleton from Dmanisi, including the complete D4167 femur and D3901 tibia, is between 145 and 166 cm. Graves' KNM-WT 15000 stature estimate is right within this range.

    Meanwhile, there was a lot of disagreement about hips.

    [Scott] Simpson and Linda Spurlock of the Cleveland Museum of Natural History realigned the pieces of Nariokotome Boy's pelvis, guided by a female H. erectus pelvis from Gona, Ethiopia, that Simpson reported 2 years ago (Science, 14 November 2008, p. 1089). They found that the widest measure from side to side on the boy's pelvis is 255 to 260 millimeters rather than 225 to 230 mm. This would give the boy an adult hip breadth of 295 to 301 mm rather than the 266 mm originally proposed, and would match those of the short, wide-hipped female from Gona, whose pelvic breadth was 288 mm. "H. erectus was not simply a small-brained modern human," says Simpson.

    Simpson's reconstruction seemed reasonable, and it's actually not that big a difference -- roughly an inch and a half (3 cm) in bi-iliac breadth. The main differences were in the overall shape of the pelvis, being shorter with a more flaring iliac blade.

    Gibbons describes the disputation that happened after Chris Ruff's presentation. Ruff has suggested that the Gona pelvis may not represent Homo -- that its broad proportions and small acetabula (hip sockets) suggest it may have belonged to an australopithecine (presumably, A. boisei).

    Much of the disagreement comes down to the estimation of femur head diameter from acetabulum breadth -- Ruff (2010) gave an estimate of 32.6 mm, Simpson and colleagues estimated between 35 and 36 mm, based on a different method. What you would want is enough acetabula of both genera to be able to examine their variation directly. We don't have such a sample; what we have are a few acetabula and several femur heads. We have the additional problem that living people seem to have a different relation of femur head and acetabulum diameters than in other anthropoids, and it's not obvious which should be applied to early hominins.

    I guess (in the relative absence of data) that this acetabulum diameter of the Gona pelvis was in the zone of overlap between Homo and Australopithecus. There's no question that later Homo -- say after 1 million years ago -- is substantially larger in acetabulum diameter, from every specimen so far described. But there are occasional small specimens of Homo even in the Middle Pleistocene. At 1.15 million years old, the Gona specimen is more than 300,000 years later than the last known occurrence of Australopithecus. The femur head that would fit the Gona acetabulum would be smaller than KNM-ER 1472 or D4167 from Dmanisi, both around 40 mm. At least one australopithecine femur head (AL 333-3) is that large, so the femur head diameter distributions do overlap. The STW 431 acetabulum diameter is a sliver larger than that of the Gona pelvis (Ruff 2010 makes it 3 mm bigger, but other workers have given a smaller estimate). SK 3155 may well be Homo and has a smaller acetabulum.

    Of course, if we go as far as SK 3155, we have to consider the topic of the Malapa innominate. Can we tell small-bodied Homo from Australopithecus on the basis of pelvic morphology? Several people writing about the Gona pelvis have made it sound like a bigger version of Lucy's. But that's not really true. The australopithecine-like appearance comes from its breadth and consequent features, including the long pubes and flaring anterior ilia. The rest? Maybe there's something here for a clever anatomist.

    UPDATE (2010-04-27): I have some e-mail about the last occurrence of A. boisei, which I wrote above was more than 300,000 years older than the Gona pelvis.

    The most potent counterargument is Swartkrans Member 1, which has uranium-lead dates around 830,000 years ago, and has been placed by many workers around a million years ago. I actually hadn't been thinking of South Africa. But it is relevant, as the East African record between 1.4 and a million years ago may not be strong enough to argue that the last occurrence of A. boisei is really very close to the extinction time.

    Meanwhile, there is OH 36, an ulna from Olduvai Gorge that may represent A. boisei. Since it's (obviously) not cranial, and is quite large and robust compared to postcranial remains that are associated with A. boisei, I've always been very skeptical of that assessment. If there's one feature of the ulna that actually has some phylogenetic importance in the Early Pleistocene, I figure it's size.

    But given the current question about body size, that reason for skepticism may have receded in importance. On the other hand, OH 36 seems to represent a substantially bigger individual than the Gona pelvis, so maybe introducing robust australopithecines into the mix doesn't help anything.

    Several things puzzle me. Even into Member 1 times, Swartkrans is dominated by A. robustus, with very little Homo. In East Africa, A. boisei is never quite so predominant in the hominin assemblage as the case in South Africa, but was nevertheless very common up to 1.5 million years ago. Did it persist much later? Was it cryptic from the point of view of the fossil record? Are the Swartkrans dates older than we think?

    References:

    Gibbons A. 2010. Human ancestor caught in the midst of a makeover. Science 328:413. doi:10.1126/science.328.5977.413

    Ohman JC, Wood C, Wood B, Crompton RH, Günther MM, Yu L, Savage R, Wang W. 2002. Stature-at-death of KNM-WT 15000. Hum Evol 17:129-141. doi:10.1007/BF02436366

    Ruff C. 2010. Body size and body shape in early hominins -- implications of the Gona pelvis. J Hum Evol (in press) doi:10.1016/j.jhevol.20 09.10.0 03

    Tags: 
    body size
    stature
    East Africa
    Homo erectus
    Malapa
    A. robustus
    pelvis
    Early Pleistocene
    Swartkrans
    Gona
    KNM-WT 15000
    A. boisei
    meetings
    Synopsis: 
    The 2010 AAPA meetings featured a fight about the Nariokotome and Gona pelves.

  • What, if anything, is Australopithecus sediba?

    Thu, 2010-04-08 22:46 -- John Hawks

    Today we finally get to learn about the exceptional discovery of four partial hominin skeletons from Malapa Cave, South Africa. Two of the fossil skeletons are described by Lee Berger and colleagues in the current issue of Science, descriptions of two more are still forthcoming.

    A kind journalist sent me a copy of the research papers a few days ago, so my graduate students and I have had a chance to think about them a little bit and compare them with other material.

    Berger and colleagues have named a new species to contain the fossils, Australopithecus sediba. For anybody who follows paleoanthropology, the new species won't be surprising -- if I found a fossil, I'd surely make up a new name for it, even if I thought it was my great-great-grandmother. In this case, the morphological reasons for naming a new species aren't trivial, but I'll begin by approaching them skeptically, especially in comparison with the large samples of South African fossils both earlier and later than Malapa. I'll conclude that a new species within Australopithecus was probably the right call, but not an easy one.

    The press is running with a "new fossils provoke debate" storyline -- are they possible ancestors of Homo or not?

    The simple answer to that question is that the Malapa skeletons are too late to be ancestors of Homo. After all, we have early Homo nearly a half-million years earlier.

    A more complicated answer is that it depends what we mean by Homo. My feeling is that these skeletons don't comport with what most of us mean when we say "Homo". Most of us have in mind an adaptive shift from Australopithecus to Homo that included larger brain size as a significant element, and the MH1 skeleton has a small endocranial volume.

    But if we accept that model of Homo, we have to accept its consequences, as the Malapa skeletons now make clear. One important consequence is that, if we assume that MH1 isn't Homo, we can no longer say have any skeletal evidence of Homo from before 1.95 million years ago. Because the Malapa specimens are more like Homo in their dental and mandibular features than are earlier specimens that have usually been called Homo.

    And if we throw out all those earlier Homo specimens...well, then suddenly Malapa isn't too old to be an ancestor of Homo after all.

    How old are they?

    The fossils lay above a flowstone with a U-series and paleomagnetic date consistent with an age just around 2 million years ago. That's a maximum age for the fossils; they must be younger than that.

    The hominins are in water-deposited sediments, which are inferred to represent ancient washes of subterranean water flows through the cave system. Two elements above the flowstone contain the hominin specimens, called facies D and E, and both have normal magnetic polarity. The most likely interpretation is that they belong to the Olduvai paleomagnetic subchron, which occurred between 1.95 and 1.78 million years ago. A specimen of the sabertooth cat Megantereon in one of these facies has a last appearance elsewhere in Africa at 1.5 million years ago. So it appears that 1.78 million years is a very likely minimum age for the fossils.

    That's about as good as dating gets in South Africa, where we're used to seeing very wide age brackets on hominin-bearing localities. It means that the Malapa hominins lived at around the same time as KNM-ER 1470 in the Turkana basin, or OH 24 at Olduvai Gorge. Until today, I think we could justly claim that the only australopithecines still known to occur in this time interval were the robust species A. boisei and A. robustus -- although the first appearance of A. robustus might (might) be later than Malapa.

    Why aren't they A. africanus?

    To me, this is the hardest question to answer.

    The Sterkfontein Member 4 sample of A. africanus is tremendously variable. The postcrania of both Malapa skeletons are tremendously informative, but fall within the range of variation at Sterkfontein for almost every feature that the authors reported. The few exceptions (such as humeral torsion and femur neck/shaft angle) are right at the edge of the Sterkfontein range.

    Malapa skeletons

    In other words, it's my impression that the postcrania of the Malapa skeletons fit within A. africanus. The limits of my impression are that there are a whole lot of observations here, and the paper generally does not report metrics for the postcrania. Maybe the sequel will give us some more surprises.

    I would have added a comparison with the Swartkrans A. robustus sample, which overlaps nearly totally in body size with Sterkfontein and contains elements that are in some cases more comparable to the Malapa skeletons. In particular, the os coxa of MH1 looks a lot like SK 3155, and the proximal femur looks like SK 82 to me, at least in the tiny picture provided with the paper. On the whole, I don't think that the Malapa hominins are particularly like A. robustus, I just think that if you put together a reasonably large sample of australopithecine postcrania, these two skeletons don't stand out.

    I'll take up the discussion of proportions of the different elements below. My feeling is that the proportions aren't exceptional for Australopithecus, either, but we have to temper that against the observation that really only AL 288-1 (Lucy) is comparable, and it's more than a million years older.

    What about the teeth? Generally speaking, the teeth of MH1 and MH2 are both at the small end of the A. africanus range. In a couple of cases (the lower canine of MH1, the lower second molar of MH2), the teeth are absolutely smaller than any Sterkfontein individual. The canines are within the range of A. robustus (remember that the robust australopithecines have small anterior teeth), but the premolars are nothing like the large, molarized Swarktrans sample of premolars.

    They're a little small but within the range of those known for Homo habilis at Olduvai Gorge. For example, OH 7 -- the type specimen of Homo habilis has molars that are 1.5 mm larger than MH1 in both dimensions.

    But then, Homo habilis really doesn't differ much in tooth size from Sterkfontein.

    In size, the Malapa teeth are exactly what you would expect for Homo erectus. The first molars are smaller than those of Dmanisi D2700/D2735, for example. But unlike H. erectus dentitions, the molars of the Malapa hominins get bigger toward the back -- M3>M2>M1.

    The Malapa mandibles are strikingly gracile. The MH1 mandible has a relatively vertical symphysis with a small cross-section. The long, parallel upper and lower corpus borders really strike me like a mandible of Homo erectus, something like KNM-ER 993 or OH 22 -- but this impression may be exaggerated considering the M3 of MH1 has yet to erupt. Metrically, the corpus breadth and height are most like OH 13. There are small australopithecine specimens that compare to this, such as AL 277-1, and it is worth remembering that MH1 is a juvenile mandible. I can't compare the ramus heights with those of other samples because the authors don't report those measurements.

    An interesting question: If these mandibles had been found in isolation, would we call them Australopithecus? The Olduvai H. habilis mandibles OH 7 and OH 13 have M3>M2>M1, while OH 16 has M2>M3>M1. The Malapa mandibles look much more like later Homo than do early Turkana basin mandibles like KNM-ER 1801, KNM-ER 1802, or KNM-ER 1482, all of which are much more robust and have larger, more molar-shaped premolars than MH1, and all of which have M3>M2>M1 except KNM-ER 1802 which lacks M3. This is a quick comparison on my part, but I think the Malapa mandibles look more like Homo than does the existing hypodigm of Homo habilis. It's hard to imagine that the mandibles in isolation would have been referred to Australopithecus. More on that below.

    Compared to the mandibles, the cranium of MH1 looks more like its counterparts from Sterkfontein. To be sure, it is an 11-13-year-old juvenile and more gracile in some respects than any of the Sterkfontein crania. But take a look at it next to Sts 71:

    MH1 next to Sts 71, frontal view

    MH1 (left) next to Sts 71 (right)

    They're not identical, naturally. Sts 71 has higher temporal lines, a slightly smaller vault, and more prominent cheeks. It also has more postorbital constriction compared to MH1, though that isn't obvious from this angle. MH1 has a true superorbital torus, Sts 71 has at best a shade of one. But you can see the similarities -- the angle of the zygomatic process of the maxilla, the narrow and concave interorbital region, the tall and narrow orbits. MH1 has no prominent anterior pillars (bony swellings on either side of the nasal aperture), but Sts 71 is not very different in this region. Sts 71 has bigger teeth.

    Consider also Sts 52:

    MH1 next to Sts 71, frontal view

    MH1 (left) next to Sts 52 (right)

    Again, Sts 52 has anterior pillars and bigger teeth, but the shape of the face is very comparable between these two. The nasal bones in particular are similar in this pair, almost "pinched" at the midline, with a lateral expansion both superiorly and inferiorly.

    We can do a similar exercise for most of the features of the MH1 cranium. What is exceptional, in the context of the Sterkfontein sample, is the overall gracility of the masticatory apparatus.

    One important thing that is not in the least bit exceptional: Its brain. An endocranial volume estimate of 420 ml (from CT reconstruction) puts MH1 at the bottom of the range of variation at Sterkfontein -- the best-known skull from Sterkfontein, Sts 5, has a volume of 485 ml, while STW 505 has a volume larger than 550 ml. Before MH1, the smallest of the South African crania were estimated to have volumes of 428 ml. This one seems to be smaller mainly by being flatter -- a shape that it shares with early Homo, but I wouldn't say it was without parallel in Australopithecus.

    But the smallest endocranial volume known for early Homo is KNM-ER 1813, at 510 ml. That specimen is extreme: the next smallest is 585.

    The vault fits in A. africanus, most of the facial features have comparable specimens in the Sterkfontein sample, with some exceptions, and the postcranial skeleton is unexceptional. The teeth are mostly within the range at Sterkfontein with some exceptions. But the mandible -- like those few facial characters -- stands out.

    Australopithecus sediba -- a new species within Australopithecus -- then seems like a fair diagnosis. The craniodental derived features are of the sort that would usually justify a new species. Heck, in the case of Kenyanthropus, even more minor differences in the face and size of teeth from contemporary A. afarensis caused Leakey and colleagues (2001) to name a new genus.

    Is MH1 really a male?

    Berger and colleagues (2010) infer that the MH1 skeleton (the one with the skull) is a male. It is large and more robust than the MH2 skeleton: Its teeth are bigger than the MH 2 skeleton, its mandible is more robust with a taller ramus, the articular ends of its limb bones are a bit larger. In addition, the greater sciatic notch on its preserved os coxa is narrower than other australopithecines like Lucy and Sts 14, and the pelvic inlet may (based on the anterior position of the auricular surface) have been smaller.

    But the skeleton isn't really very big. Its endocranial volume is small, its long bones are not nearly so robust as some australopithecines. There are large male australopithecine skeletons -- STW 431, for example -- and MH1 doesn't seem so large as these. Again, it's hard to tell without postcranial measurements, but the sex of this specimen isn't a clear call either way.

    The sex of the specimen is important to the way we interpret it, because the features that make it stand out from A. africanus concern masticatory gracility. If it's a female, it doesn't seem quite so different from A. africanus as if it's a male.

    Are they Homo?

    Let's start with the brain size, which at 420 ml seems to be the most obvious thing separating MH1 from our genus. Well, except for Liang Bua 1 -- with its endocranial volume of, um, 420 ml. Is brain size fundamental to Homo? Maybe. Maybe not.

    Alan Boyle's report on the fossils ("Fossils shake up our family tree") has an excellent letter from Don Johanson, who makes the argument that the Malapa fossils should be assigned to Homo. Of course, Johanson and Bill Kimbel in 1996 described a 2.33-million-year-old fossil from Hadar as the earliest clear maxilla of Homo. That maxilla, AL 666-1, resembles Homo in having a more vertical subnasal profile, a parabolic dental arcade, molars that are long relative to their breadth, and a "squared-off" jaw that is relatively straight across the anterior dentition. In other words, basically the dental features seen in the MH1 maxilla.

    We've got two choices. Maybe these are genuine shared derived features with these specimens and Homo -- in which case, we should probably name them Homo, as Kimbel and colleagues did for AL 666-1.

    Or, there were several australopithecines after 2.5 million years ago with these dental and maxillary (and for the Malapa hominins, we can add mandibular) characters. In which case, they're not signs of Homo at all. They may reflect parallel dental reduction in several australopithecine lineages, all of which faced niche differentiation from the emerging robust australopithecines. One of those lineages may have given rise to Homo, but we don't know which. Maybe it was South African, but it need not have been. It could even have been Asian.

    The question is just how important we think brain evolution was to the origin of our genus. If the brain was the key adaptation, then Malapa shows that the dental features are irrelevant to the brain -- because these skeletons have more dental reduction than most of the East African Homo habilis sample, but MH1 has a much smaller brain.

    What about tool manufacture?

    Part of the logic of pre-2-million-year-old Homo is the emergence of stone tool manufacture 2.6 million years ago. It stands to reason that this major shift in behavior and diet might have given rise to a new adaptive plateau for early hominins, and that would have been tied to the evolution of larger brains. The problem is that we don't have larger brains in any fossil remains until after 2 million years ago -- KNM-ER 1470 remains the earliest hominin with a brain larger than 600 ml. Up to now, people have conjectured that large-brained hominins may have existed earlier, even to the point of arguing about the brain size reflected by the otherwise-robust temporal bone from Chemeron. But it's worth pointing out that none of these pretenders to the Homo throne have smaller teeth than A. africanus. The diet shift that should have been made possible by a meat-eating stone tool economy didn't lead to smaller teeth until much later.

    And now we know that at least one small-toothed hominin also was a small-brained one.

    We don't know whether the Malapa hominins would have been toolmakers. The fact that they weren't found with tools isn't really evidence either way. Dirks and colleagues (2010) suggest that the skeletons were deposited by water washing them from an initial death trap into a secondary location. If true, it would be a miracle beyond belief for stone artifacts to have made the trip with them.

    We do know that stone tools are present in Sterkfontein Member 5 and Swartkrans Member 1, and cutmarked fauna are in the latter. Both these may be roughly contemporaneous with the Malapa hominins, depending on their date. So toolmaking hominins were in the immediate area, around the time that the Malapa hominins lived.

    SK 847 is from Member 1 of Swartkrans, and could be as old as the Malapa skeletons. Its endocranial volume isn't known, but facially it looks even more like Homo erectus than does MH1. It seems plausible that this skull represents the local toolmaking population, but even so, this skull does resemble MH1 in several respects, and again we don't know its volume. STW 53, probably a bit older than Sterkfontein Member 5, has also often been referred to Homo but it definitely doesn't have a substantially larger endocranial volume than MH1.

    So again, we seem to be faced with two choices: Broaden the definition of Homo to include this very australopithecine-like sample, or restrict it to later large-brained hominins. In either case, brain size and tool manufacture do not necessarily go together.

    What's the single most obvious thing that the paper doesn't describe?

    Which brings me to the fingertip. MH2 has a distal phalanx. The paper doesn't describe it, even though this bone element has taken on such importance in the evolution of Homo compared to Australopithecus. Big fingertips are supposed to be adaptations to force transfer through the fingertip grip used in tool manufacture.

    The picture of the thing is so tiny -- I mean, literally we're talking about two pixels of finger -- that I can't make anything out of it. Does it have a large apical tuft, like OH 7? Or is it like the Hadar distal phalanges, with narrow, apelike apical tufts?

    If one was wondering about whether the thing was Homo or not, I would think this is one of the first things you would check....

    What about those limb proportions?

    For fifteen years, a bunch of otherwise sensible paleoanthropologists have been engaged in a debate about the limb proportions of A. africanus and H. habilis. The reason why this particular question may not be sensible is because the debate is about the length of the arm relative to the leg, but there's no specimen of A. africanus that preserves both the length of the arm and the length of the leg.

    What there are: OH 62, a skeleton apparently of H. habilis that has a complete humerus and more than half the length of one femur, STW 431, which has an acetabulum and mostly complete humerus, and Sts 14, which has a partial femur, an acetabulum, and a piece of distal radius. On the basis of these fossils, we've seen some intense debate about the reconstruction of the OH 62 femur length, and a lot of discussion about whether the sizes of articular surfaces are relevant to the function of the limbs. Indirectly, it has appeared that A. africanus and H. habilis shared longer arms than were present in AL 288-1 (Lucy).

    Well, now we have two fossil skeletons with both hindlimb and forelimb elements. The paper doesn't address the issue directly, nor does it provide raw measuremnets that would lead to a quick answer. But the humerus is short relative to the size of the femur head, compared to earlier hominins, while a bit long relative to Homo by the same comparison. So it looks like the Malapa skeletons may be somewhere in between.

    The authors do argue that OH 62 is an odd skeleton in one respect: They consider the "diaphysial strength" of the humerus and femur. This is a cross-sectional measure of the area of cortical bone, and reflects the robusticity of both forelimb and hindlimb elements. In their estimation, OH 62 has a much stronger arm relative to its leg strength than the Malapa skeletons.

    It's not obvious how to interpret this observation. Is OH 62 more apelike in its locomotor pattern than Malapa? Or does the strength ratio vary allometrically with body size, and OH 62 is just at the smallest end of the comparison? Hard to tell without the length measurements.

    OK, what's the bottom line?

    Here's the important thing. From today forward, there are a bevy of features of the face, teeth and jaw that are no longer "derived characters" of Homo.

    Some people will want to fix this by broadening the definition to Homo to include the Malapa skeletons. Others will want to narrow the definition of Homo to include only large-brained specimens.

    Every specimen attributed to Homo before 2 million years ago is now up for grabs. Maybe they're Homo, or maybe their resemblances to Homo are just masticatory parallelism. We already know that parallelism explains many of the derived locomotor and masticatory resemblances of great apes, and many strongly suspect that parallelism explains the derived masticatory resemblances of robust australopithecines. If the dental reduction that once was a marker of Homo joins this list, it will hardly be surprising.

    If we follow the logic that connects tool use to dental reduction, however slowly and indirectly, then I think we have to conclude that A. sediba was likely a toolmaker and meat-eater. This hypothesis is testable, both by bone chemistry and dental morphology and wear.

    Malapa suggests the hypothesis that brain evolution followed the appearance of stone tool manufacture by a considerable delay. If so, I wonder what exactly caused the brain to expand. Did the diet shift to higher-quality foods unfold over a long time, allowing brains to expand only after 3/4 million year delay? Or was brain evolution caused mostly by non-dietary factors, such as social dynamics or climate instability?

    Or did the evolution of our genus happen somewhere else, far from the places where we currently have fossil samples? The Rift Valley and South African cave systems may have been wonderful for preserving fossils, but who's to say they weren't relative backwaters when it came to the evolution of Homo?

    Well, I'm running out of gas for this installment. More later....

    References:

    Berger LR, de Ruiter DJ, Churchill SE, Schmid P, Carlson KJ, Dirks PHGM, Kibii JM. 2010. Australopithecus sediba: A New Species of Homo-Like Australopith from South Africa. Science 328:195. doi:10.1126/science.1184944

    Dirks PHGM, Kibii JM, Kuhn BF, Steininger C, Churchill SE, Kramers JD, Pickering R, Farber DL, Mériaux A-S, Herries AIR, King GCP, Berger LR. 2010. Geological Setting and Age of Australopithecus sediba from Southern Africa. Science 328:205. doi:10.1126/science.1184950

    Tags: 
    Malapa
    A. sediba
    South Africa
    Homo erectus
    locomotion
    diet
    Homo habilis
    A. africanus
    tool manufacture
    Australopithecus
    Synopsis: 
    New skeletons from Malapa, South Africa, present surprising evidence about the evolution of our genus.

  • Mailbag: Variation in stature

    Thu, 2010-01-21 15:32 -- John Hawks

    Re: "The changing height of Homo erectus":

    I was looking through today’s Redeye (Chicago Tribune’s mini paper) and saw a picture of the world’s shortest man (He Pingping of China) holding the finger of the worlds tallest man (Sultan Kosen of Turkey) and I thought if a paleoanthropologist dug these two up near each other they would never assign them to the same species. I wonder just how many finds have been misinterpreted and are actually the same species. I have definitely come around to the idea of anagenesis and I wonder if you could squeeze in something about Homo heidelbergensis perhaps in one of your post on Neanderthals or something. Did they evolve into moderns or die out?

    Well, H. heidelbergensis is certainly a can of worms.

    Here's a start: If we and Neandertals descend from a single population that lived 350,000 years ago or so, where did that population live? If Africa, what does that make the Sima de los Huesos sample, at 600,000 years old? If Europe + Africa, then why was its genetic variation so low, and how was this continuity maintained? And, if it was, why would we assume modern humans aren't part of this continuous population?

    This is the difficulty.

    Meanwhile re: variability -- we may be near that point already. Consider that "H. erectus" now includes adult specimens with endocranial volume of 600 ml and others with 1200. That doesn't exceed the extremes of normal human variation, but it is very unlikely you'd find this amount of difference in an equivalent sample size of humans. Or chimpanzees. Or gorillas.

    Tags: 
    Homo heidelbergensis
    stature
    Homo erectus
    Neandertals

  • The changing height of Homo erectus

    Wed, 2010-01-13 14:00 -- John Hawks

    Gretchen picked up a partial set of Time-Life volumes, from 1973, part of the series "The Emergence of Man". She found them at a garage sale. There's a lot of fun stuff in them, and some very useful illustrations.

    For example, I'm looking through the volume titled, The First Men, which is basically about Homo erectus. The meat of the book is a series of descriptions of fossil and archaeological finds -- Dubois on Java, Terra Amata, Torralba and Ambrona. No surprise, each of these has a very different theme than we would give them today!

    Here's a fun comparison:

    Body proportions of fossil hominins, from 1973

    This is a two-page spread in the book; really a fine illustration by Roger Hane.

    Homo erectus, in the middle, is reconstructed with a stature pretty much right in between Australopithecus and Homo sapiens.

    If you open up most recent textbooks, you'll find Homo erectus illustrated as the same height or taller than us. This is mostly due to the KNM-WT 15000 (Nariokotome) skeleton, discovered in 1984. This skeleton was estimated to have a moderately tall adult stature -- around 185 cm (6 feet 1 inch). There are three or four other femora from the Lower Pleistocene that also correspond to stature estimates up around 180 cm, in particular KNM-ER 736 and KNM-ER 1808.

    Now one might reasonably wonder, what's the big deal about 185 cm? The Nariokotome skeleton hardly represents a giant -- at 6'1" he would have been an inch shorter than me, for goodness' sake! And with only one fossil specimen within 2 inches, it shouldn't be churlish to point out that the Nariokotome estimate is not based on a real femur length -- it's an estimate based on an estimate. Most Lower Pleistocene fossil femora were much shorter, and yield stature estimates well under 180 cm. So why did anthropologists so eagerly cling to the tallest estimates for Homo erectus?

    Few Lower Pleistocene postcranial bones are associated with skulls, so it's difficult or impossible to assign smaller bones to a species. How do we know whether a short femur belongs to Homo erectus or Homo habilis -- which we know from OH 62 is much smaller in body size? Or A. boisei, which it would appear from KNM-ER 1500 is also smaller? We don't really know -- so the bones that correspond to mid-range stature estimates, say around 160 cm, might belong to any of the above. But the tall ones -- well, we know that those must represent the largest-bodied hominin. So there was a tendency to assume that the tall specimens were near the average for Homo erectus.

    It was a hypothesis. It has turned out to be false.

    The illustration in the Time-Life book is based on entirely different fossils. The Turkana fossils were unearthed during and after the early 1970's. Before that, Homo erectus stature could be estimated from the Trinil (Java) and Zhoukoudian (China) femora. These are later than the early African Lower Pleistocene sample. The Zhoukoudian femora in particular give stature estimates at or under 5 feet (152 cm). We might read it as a decline, and some people did as recently as 5 years ago. But the Dmanisi postcrania are also short, a bit shorter than the Zhoukoudian femora. And they're earlier than Nariokotome. And we now know of smaller crania of Homo erectus in the East African Lower Pleistocene. So the tallest statures aren't the average; they're the tallest.

    It ain't rocket science, I know. But this is progress.

    Today, I think it's fair to say that the variation of stature in Homo erectus was more or less like the variation within living people. There are short and tall populations today, varied in ecology and latitude. The average stature of young men in the Netherlands today is 184 cm. Adult women in the Philippines average only 150 cm. So the best way to compare statures is to illustrate the range.

    That being said, I don't think we know how stature has evolved over time. We do have some data points -- the Neandertals were shorter than Upper Paleolithic Europeans, for example, but seem to have been around the same height as Mesolithic people (and a shade taller than Neolithic Europeans). The Dmanisi people were on the short end of the human range, but not unusually so. The variability within Lower Pleistocene East Africans seems high, but I'd want to see a serious test compared to human populations.

    It's a case in the fossil record where discovering more seems to have resulted in us knowing less. But that's just because we can now reject several categorial statements that people used to accept uncritically.

    Related articles:

    "News flash: Dmanisi hominids were not short"

    "Body size in Holocene South Africa"

    Body mass in ancient humans and high-latitude populations

    Tags: 
    Zhoukoudian
    Dmanisi
    Nariokotome
    Turkana
    Homo erectus
    stature
    Synopsis: 
    The re-evaluation of the stature of KNM-WT 15000 provokes a "blast from the past", looking at the statures of other Homo erectus specimens.

  • My Leiden adventure

    Thu, 2009-12-03 09:59 -- John Hawks

    I've just returned from a week in Leiden, the old university city of the Netherlands. I was a guest of the archaeology faculty, in particular Wil Roebroeks and his stable of students and postdocs, and they were fantastic hosts. I can't say enough about the new friends I have in Leiden.

    Except maybe that they set an awfully high bar for the next place I get to visit!

    Dutch windmill

    There was excitement in the whole country as the Naturalis museum opened the first exhibition outside Georgia of the D2700 skull from Dmanisi. The TV news covered David Lordkipanidze arriving with the skull, and followed his entourage from the airport. The daily newspapers carried huge broadsheet stories about the fossils and the exhibition. It was pretty cool.

    I only wish Lucy had gotten anything like that kind of reception in the States.

    I played a small part opening the exhibit by participating in the public lectures at Naturalis on Saturday. There was a very energetic crowd of ticketholders, eager to hear about the science of early humans and to attend the exhibit.

    The skull and its mandible D3735 are displayed in the "Treasure Room" of the museum:

    D2700 at Naturalis

    The museum houses the original Dubois fossil collections from Trinil, Java, including the Pithecanthropus skull and femur. If you visit, you can see the originals on display:

    Trinil skull

    I sat down alone with them for a while during the gala reception and did what comes naturally:

    Trinil skull sketch

    Unfortunately, spending a week in the Netherlands meant that I had to miss our Thanksgiving at home. Gretchen thinks we should have turkey in the next week or two to make up for it, and I'm not complaining. On the date, however, I got a real authentic Pilgrim experience, as I stayed just above the American Pilgrim Museum in Leiden:

    The Pilgrim Museum of Leiden

    Such a unique place, with incredibly nice proprietors!

    So, blogging has been slow as I was soaking in the surroundings, and giving my hosts a preview of some of the research that will be coming out in the next year or two. They've told me that they'll feel paid amply if I keep doing what I do here. So let's get back to it!

    Tags: 
    Homo erectus
    media
    Hawks sightings
    museums
    Dmanisi
    travel
    site
    Trinil
    Synopsis: 
    I'm given the royal treatment during a visit to one of the oldest universities in Europe.

  • Oh, the meganthropy!

    Mon, 2009-11-23 01:21 -- John Hawks

    Taxonomic confusion afflicts a hapless victim hunting for Homo erectus:

    In the seeming middle-of-nowhere, we found a monumental, but rather neglected, concrete marker to another even earlier hominid, Meganthropus paleojavanicus, who lived there around 1.5 million years ago.

    But it was all, it has to be said, a bit of an anti-climax.

    A somewhat more helpful report on the Sangiran Museum can be found at Planet Mole.

    Tags: 
    Java
    Homo erectus
    Sangiran

  • It came from Guangxi

    Mon, 2009-11-02 00:40 -- John Hawks

    Science journalist Richard Stone writes in the current Science about new Late Pleistocene skeletal remains from Guangxi: "Signs of Early Homo sapiens in China?"

    The big prize is the Homo mandible, whose owner would have had a chin that curved ever-so-slightly outward. H. erectus had an inward-sloping chin, whereas modern human chins generally jut out farther than the Guangxi specimen's. Jin's group classifies the fossil as primitive H. sapiens and says the intermediate chin suggests interbreeding with H. erectus. Uranium isotope dating by R. Lawrence Edwards of the University of Minnesota, Twin Cities, indicates that the fossil-bearing layer is about 110,000 years old, in a paper that will appear in the November issue of Chinese Science Bulletin.

    The article frames the discovery as a challenge to the "Out of Africa" hypothesis of modern human origins, thereby giving the "out of Africa" defenders several chances to rebut. That framing comes from the discoverers, who are pushing the "early modern" aspects of the jaw.

    I don't think the modern/nonmodern classification is very productive. Here's a mandible with a chin -- a small chin, but apparently a real mental trigone (the article is accompanied by a photo, not the greatest). It's no less "modern"-looking than most of the 100,000-year-old Klasies River Mouth mandibles (thanks to a reader for noting that one). Some Neandertals had chins, and some much earlier humans came pretty darned close. A chin is not a diagnosis, it's a symptom.

    Here's a better question: what explains the epidemic? The same anatomical feature, showing up in widespread geographic locations within the past 100,000 years? If these populations were isolated with no gene flow between them, the chin must have appeared coincidentally by convergent evolution. The other alternative is that these ancient human populations traded some genes.

    How unlikely is the chin, really? Is it a developmental side effect of a single genetic change? Would that make it more likely, because no combination of factors is required? Or less likely, because a single mutation causing such a strange effect would be very improbable to begin with?

    References:

    Stone R. 2009. Signs of Early Homo sapiens in China? Science 326:655. doi:10.1126/science.326_655a

    Tags: 
    Asia
    Homo erectus
    Late Pleistocene
    early modern
    China

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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.