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paleoanthropology, genetics and evolution

recent evolution

  • Falciparum malaria came from gorillas

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

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

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

    From the discussion:

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

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

    References

    1. Liu W, Li Y, Learn GH, Rudicell RS, Robertson JD, Keele BF, Ndjango J-BN, Sanz CM, Morgan DB, Locatelli S, et al. 2010. Origin of the human malaria parasite Plasmodium falciparum in gorillas. Nature [Internet] 467:420–425. Available from: http://dx.doi.org/10.1038/nature09442
    Tags: 
    parasites
    recent selection
    disease
    gorillas
    Africa
    recent evolution
    malaria
    chimpanzees

  • Mailbag: The teacher who wouldn't believe in shrinking brains

    Wed, 2010-09-15 15:54 -- John Hawks

    My son, a student at [redacted university], was recently ridiculed by his professor in class when my son suggested that the human brain has been shrinking for the last 20,000 years (the teacher insists that it has not changed). When my son cited the article in September Discover, he was (somewhat understandably) further ridiculed for such a source. My question is: can you provide me with some links to credible sources for this information? He has started to work on this, but wading through so many sources that mention brain size, etc. has proven difficult. We would appreciate any help you could provide.

    Thank you for writing -- that is indeed sad but not surprising; I hear all too often from people who have teachers that can't be bothered to read.

    The reduction in brain size during the last 10,000 years is a really well-known fact in anthropology, it is not at all controversial. It is, for example, discussed in the introductory-level textbook that I assign my students. I have attached several papers that include primary data from archaeological or historical samples. In Europe the trend is most clearly documented, because of the large number (many thousands) of skeletons that have been studied, but the trend is also apparent in South Africa, China, and Australia. Some of the papers include many other characters that also changed during the same time span.

    We cannot rule out that other locations might have had stasis instead of reduction in brain size, but there is not yet a well-documented example of it.

    The most common explanations for a reduction in brain size are (a) diet and the consequent reduction in body size; and (b) warmer Holocene climate. Larger brains are always bad, in that they require more development and time, so what we are looking at in the Holocene is a change in the stabilizing selection -- either an intensification of selection against larger brains, or a relaxation in selection against small brains.

    Body size also did get smaller during the past 50,000 years, which gives rise to the question of whether the brain has reduced *more than should be expected* from the reduction in body size. My research indicates that it has done so (this was one topic covered in the Discover article), but I would not say this is yet a consensus view.

    Tags: 
    brain
    Holocene
    recent evolution

  • Mailbag: Remaking

    Wed, 2010-02-24 07:20 -- John Hawks

    Found this
    "The Earth is not finished, but is now being, and will forever more be-remade."
    (C.R. Van Hise, 1898)
    "Human evolution is not finished, but is now being, and will forever more be-remade."

    Reminds me of Darwin's last line in the Origin...

    Tags: 
    recent evolution
    quotes

  • Genes and archaeology

    Tue, 2010-02-23 21:33 -- John Hawks

    Current Biology has released a special issue titled "Global genetic history of Homo sapiens". There is much of interest in this issue, with seven papers, mostly regionally focused in different parts of the world, but one paper by Jonathan Pritchard and colleagues discussing recent adaptive evolution.

    The geneticists to varying extents in this volume depend on archaeological observations, but in many cases read the archaeology very selectively. Speaking as someone who takes archaeology seriously, I find this very frustrating. With more genetic data, we need to demand

    An editorial by archaeologist Colin Renfrew leads off the special issue ("Archaeogenetics -- towards a 'new synthesis'?").

    Today, we have an abundance of data about the genetic variation of living people that we did not have ten years ago. In addition to our samples from living populations, we are beginning to find a trove of information about ancient people, from DNA extracted directly from skeletal material. But despite the attempts of geneticists and (rather pitifully few) archaeologists, I don't see a "new synthesis" emerging.

    Reading the first paragraph of his editorial, it seems to me that Colin Renfrew agrees:

    It seems a timely moment to review human population history of the five continents as it emerges from recent archaeogenetic studies, as summarised in the reviews of this special issue of Current Biology. Has the ‘new synthesis’ — between genetics, archaeology and linguistics — arrived which I, perhaps incautiously, heralded a few years ago [1]? These highly informative reviews document, it seems to me, both achievement and uncertainty: the achievement relates to the remarkably consistent picture which has now emerged about the out-of-Africa emergence of our own species Homo sapiens and the initial peopling of the Earth. The uncertainty involves the application of archaeogenetics to the more recent, Holocene period, when most of the planet was already peopled — except much of Oceania — and sedentary, farming-based communities emerged. Here, it appears that much of our current understanding still depends on archaeological or, sometimes, linguistic evidence. And, with a few exceptions, the archaeogenetic evidence has not yet been assimilated into a genuine synthesis; but, let us begin with the good news.

    I find it a markedly bad sign that Renfrew thinks the best of "archaeogenetics" is the part with the least archaeological evidence. If the genetics doesn't seem to work where there is abundant archaeology, why should we believe the genetics in cases where the archaeology is poor?

    I write that quite seriously, as someone engaged directly with the genetics. It's too easy to make stuff up. How can you test a hypothesis that seems consistent with genetic data? The obvious approach is to try to falsify the hypothesis with archaeological observations -- but sadly, archaeology is often pitifully silent on the subject of demography and gene flow, or there are many scenarios equally consistent with the same archaeological record.

    In the Holocene, archaeology has a lot of power to rule out hypotheses about demography and population movement. So this is where I want to see serious attempts to falsify archaeological models using genetics. And that's what we're starting to get! The finding from ancient DNA that early European farmers were neither closely related to earlier hunter-gatherers nor to later agriculturalists has been very surprising. It seems to reject the hypothesis that today's gene distributions come from an initial dispersal of farmers with their Indo-European languages -- the European component of the so-called "language-farming hypothesis".

    Why? Well, because a later massive genetic change suggests that the language transition may well have happened a lot later (as suggested by much of the linguistic evidence itself), and the mtDNA haplotypes carried by the early European farmers have no clear relationship to Near Eastern or central Asian populations.

    It's no surprise that Colin Renfrew would find disagreements with this genetic work; he's the biggest supporter of the "language-farming hypothesis".

    But I think that the current situation is very healthy. Geneticists are testing hypotheses and showing them to be false. At the same time, they're proposing models that archaeology can easily show to be false. For example, many recent evaluations of adaptive evolution have looked for genetic outliers against a "neutral" population model that involves very small Holocene population size. From the genetic perspective, this small population size assumption is conservative -- it means that some genuine cases of adaptive evolution will look less statistically significant. But archaeology can actually inform us about these cases. Any scenario in which the Holocene population was smaller than millions of individuals must be false. In many cases, a less conservative model is in order.

    I think there are tremendous opportunities for integrating adaptive evolution remains to be integrated with our understanding of demography. I don't put a lot of faith in the current storyline about genetics and the earlier part of prehistory. That story will continue to develop as we deepen our understanding of the demographic and adaptive factors that have shaped human genetic variation within the last 50,000 years.

    References:

    Renfrew C. 2010. Archaeogenetics -- towards a 'New Synthesis'? Curr Biol 20:R162-R165. doi:10.1016/j.cub.2009.11.056

    Tags: 
    genomics
    recent evolution
    Colin Renfrew
    mtDNA migrations
    acceleration

  • Mailbag: Haplogroups of Peruvian mummies

    Sat, 2010-02-20 20:31 -- John Hawks

    Now that we have looked at the DNA of the Tarim Basin mummies, when is somebody going to do the same for the mummies found at Paracasa, Peru? I know that anyone who is interested in them is considered a crank or a racist, but dammit--they do look very Caucasian. The hair is not just just light colored, but very fine and wavy in texture. The funerary masks sometimes have blue-colored stones embedded in them to represent the eyes.

    If they do turn out to be Caucasian, it could be the biggest story in anthropology in a century. They could be a remnant population of our paleolithic ancestors if the Folsom/Solutrean hypothesis is true. Or if they are more recent arrivals, they could show some affinities for some still extant population. Greeks, Romans, wandering Irishmen? Who knows? I don't have any axe to grind in this, I just want to know where such unusual looking people came from.

    There has been some ancient DNA work on ancient Paracas culture mummies, Dienekes wrote about this a little bit last year:

    http://dienekes.blogspot.com/2009/07/mtdna-from-pre-columbian-peru.html

    ..and I found a few more references. There are none but the usual South American mtDNA haplogroups, but that leaves quite a bit of uncertainty about the relationships of the ancient and living populations, which apparently differ substantially in frequency. The same is true in Europe between Neolithic and recent samples. Whole-genome sequencing will be very interesting, not least because the South Americans should have different recent selection histories compared to Old World populations.

    Tags: 
    South America
    recent evolution
    ancient DNA

  • Mailbag: Hidden lactase persistence alleles?

    Sat, 2010-02-20 12:15 -- John Hawks

    I just noticed this new article that I thought you might be interested in, suggesting that lactase persistence known genetics can't currently wholly explain the trait in large regions around Africa and Europe:

    http://www.biomedcentral.com/1471-2148/10/36/abstract

    Thanks. I've been studying that one for a couple of days. It looks like pretty suggestive evidence that there should be some as-yet-undiscovered lactase persistence allele in West Africa, or maybe a gene conversion from one of the already-known African mutations.

    See also Razib on this paper:

    http://scienceblogs.com/gnxp/2010/02/what_genes_cant_tell_us_about.php

    Tags: 
    Africa
    recent evolution
    diet
    recent selection

  • Is modern man a "wimp"?

    Tue, 2009-10-20 00:38 -- John Hawks

    That's the conclusion of a Reuters article, which describes a book by Australian science writer Peter McAllister. The book is titled, Manthropology: The Science of the Inadequate Modern Male.

    At some level, there's no denying that Nature doesn't make men like she used to. As I detailed in Slate last spring, our skeletal muscles have half the strength of chimpanzee muscles, holding their mass constant. Neandertals were comparatively stocky and muscular -- especially compared to their mass -- leaving modern human hunter-gatherers in the dust.

    But Neandertals weren't built like modern-day weightlifters. So I'm always skeptical when I see direct comparisons of ancient and modern people. The changes aren't always in the direction you might assume.

    McAllister's bottom line is perfectly accurate:

    "The human body is very plastic and it responds to stress. We have lost 40 percent of the shafts of our long bones because we have much less of a muscular load placed upon them these days.

    "We are simply not exposed to the same loads or challenges that people were in the ancient past and even in the recent past so our bodies haven't developed. Even the level of training that we do, our elite athletes, doesn't come close to replicating that.

    Not all the skeletal changes in recent populations have been caused by plasticity; there are some good reasons to think that our recent gracility is a product of evolutionary change. But it is entirely true that our bone cross-sectional areas have greatly reduced, with consequent reductions in compressive and torsional strength. We don't suffer the stresses of the past, and our bones are weaker than ancient peoples' -- at least in comparison to our mass.

    That's the complicated part of any comparison -- men in Westernized nations today tend to be bigger than many ancient groups of people. If you're going to compare "wimpiness" between Neandertals and living men, you have to understand the relative masses.

    Let's take McAllister's example of a hypothetical body-building Neandertal woman:

    McAllister said a Neanderthal woman had 10 percent more muscle bulk than modern European man. Trained to capacity she would have reached 90 percent of Schwarzenegger's bulk at his peak in the 1970s.

    "But because of the quirk of her physiology, with a much shorter lower arm, she would slam him to the table without a problem," he said.

    The shorter lower arm is clearly true -- Neandertals had short arms, and particularly short lower arms. But today's women have short lower arms compared to men, and they don't routinely win arm-wrestling contests. It does come down mostly to muscle.

    Did Neandertal women really have 10 percent more muscle bulk than modern European men? At 60-80 kg in mass, Neandertal women were between the 5th and 50th percentiles for American white men (link). Neandertals were leaner than American men today, but females are not as lean as males. Women today have a muscle mass between 15 and 25 kg; men between 20 and 40 kg. Conceivably, a Neandertal woman would have been comparable to today's men in terms of muscle mass, but I don't see an obvious basis for the idea that Neandertal women were 10 percent more muscle-bound than men today.

    What about speed?

    His conclusions about the speed of Australian aboriginals 20,000 years ago are based on a set of footprints, preserved in a fossilized claypan lake bed, of six men chasing prey.

    An analysis of the footsteps of one of the men, dubbed T8, shows he reached speeds of 37 kph on a soft, muddy lake edge. Bolt, by comparison, reached a top speed of 42 kph during his then world 100 meters record of 9.69 seconds at last year's Beijing Olympics.

    In an interview in the English university town of Cambridge where he was temporarily resident, McAllister said that, with modern training, spiked shoes and rubberized tracks, aboriginal hunters might have reached speeds of 45 kph.

    Usain Bolt's 10m split times in the 2008 Olympic 100m race are posted here. The top speed of just over 42 kilometers per hour corresponds to a 10m split of 0.82 seconds.

    A speed of 37 kph would correspond to a 10m split of 0.97 seconds. If the ancient Australian ran the same 100m race profile as Usain Bolt, with split times based on the proportion 0.97/0.82 compared to Bolt's, the 100m time would be 11.46 seconds, compared to Bolt's 9.69.

    The Wisconsin high school track record 100m time is 11.84 seconds. For girls. The boys' record is 10.27 seconds.

    Now I'm not saying that 37 kph isn't an impressive speed -- there's no way I could run that fast, even if I were being chased by a Sasquatch. My point is just that there isn't very much time separating a good high school athlete from the World Record. Sprinters spend an intense effort training to shave a miniscule fraction off their times.

    Maybe it's true that modern shoes and a good training regimen could have made this ancient Australian into a Bolt-beater. Several aboriginal Australians have become world-class track athletes. Running with bare feet on natural substrates is tough -- although some modern track athletes have preferred to train that way.

    But it's hardly a knock against "modern males" to say that ancient footprints would have crossed the finish line a second slower than the fastest Wisconsin boys.

    Anyway, the article notes a few more anecdotes from the book. On the whole, it sounds like the book has some interesting stories. McAllister may be on safer ground with many of his ancient historical cases -- the marvelous endurance of Athenian rowers and Roman legionnaires, for example. The main idea is the recent decline in skeletal robusticity, which is well documented.

    Tags: 
    recent evolution
    sports
    books
    social
    Synopsis: 
    The book "Manthropology" suggests that our ancestors were hardier than us, in sometimes cockamamie ways.

  • Body size in Holocene southern Africa

    Mon, 2006-02-13 23:04 -- John Hawks

    I was just taking notes on this paper by Sealy and Pfeiffer (2000), and found some good quotes about body size in the Bushmen, both historically and in archaeological samples:

    Historical and ethnographic sources consistently indicate that Khoisan peoples were and continue to be petite. A group of early-20th-century San studied by Dart (1937a, b) had mean statures of 155.8 cm (males) and 146.1 cm (females). Decades later, the Harvard Kalahari study found mean statures of 160.9 cm (males) and 150 cm (females). These values are comparable to the fifth centile of adult stature for contemporary North Americans (Abraham 1979). Adult weights reported for the more recent individuals are 47.9 kg (males) and 40.1 kg (females) (Truswell and Hanson 1976).

    It has been claimed that environmental stressors, especially shortages of food, affected growth (Dornan 1975:80; Almeida 1965:6). The secular trend towards increasing stature among mid-20th-century Khoisan (Tobias 1978) could be seen as evidence for the influence of environmental factors.

    At the same time, there is a genetic component. Low stature persists even under apparently favourable health conditions. The small body size and lean physique of living Khoisan peoples are often cited in human population biology texts as exemplary of adaptation to a hot, sometimes specifically desert, climate. Their low body-mass index is portrayed as support for Bergmann's and Allen's rules (cf. Molnar 1998, Relethford 1997). Through study of archaeologically derived materials, these hypotheses can be explored.

    That's on the historic record. They examine a number of skeletons from archaeological sites and report this:

    Dimensions of selected bones from the southern Cape sample are summarized in table 2. Data from one exceptionally small skeleton (UCT 345, probably a dwarf) and the three most recent skeletons with anomalous isotope values (Sealy 1997) are not included in the summary statistics for body size. The mean stature calculated from 20 male femora is 157.8 cm (s.d. = 7.9). Twenty-three female femora have a mean estimated stature of 146.9 cm (s.d. = 10.5). Greater variability among females results from some very small individuals between 4,000 and 2,000 B.P. (see fig. 4). Body size, represented by femoral head diameter to maximize sample size and divided into five sex categories, is plotted against radiocarbon date in figure 5. This figure illustrates that the smallest individuals (femora

    That's 4'10'' for females; 5'2'' for males in the archaeological sample. Bi-iliac diameter for males was 214.6 ± 16.8, for females 209.0 ± 12.3.

    Tags: 
    recent evolution
    Africa
    Holocene
    body size
    hunter-gatherers
    South Africa
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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.