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paleoanthropology, genetics and evolution

Holocene

  • Recent evolution and future evolution

    Mon, 2006-04-10 23:04 -- John Hawks

    Wired has a short article by Annalee Newitz about recent evolutionary changes and their implications for futurists:

    "I think my work is changing people's ideas about evolution, because now natural selection seems to have continued all the way up to the present day," said [Jonathan] Pritchard. "There's no reason to think it stops now."

    That's why futurists like [Ray] Kurzweil are excited about Lahn and Pritchard's work -- it could lay the foundations for a new understanding of evolution that's more tolerant of the idea that humans should intervene in their own genetic transformation.

    [Bruce] Lahn is comfortable with this idea. "If there's an evolutionary advantage to be had by using technology, then people will do it," he said. "People are going to start changing the game in evolution in ways Darwin never anticipated."

    Trans-humanist pundit James Hughes, author of Citizen Cyborg, thinks it's time to speed up the evolutionary process.

    "You can take what nature gave you, but there's no good reason to take nature as a guide for where you should go in the future," Hughes said.

    Now, that's an angle I hadn't thought of, and I've been thinking about this a lot. But it does make sense -- there's nothing inviolate about being human in the way we are now, since humans keep on changing.

  • The rats of Easter Island

    Sun, 2006-03-12 21:55 -- John Hawks

    A new article in Science is claiming that the Easter Island population did not have a long duration on the island, and probably did not cause its own population crash.

    There is a LiveScience news account by Ker Than, with some great quotes:

    Lipo thinks the story of Easter Island's civilization being responsible for its own demise might better reflect the psychological baggage of our own society than the archeological evidence.

    "It fits our 20th-century view of us as ecological monsters," Lipo said. "There's no doubt that we do terrible things ecologically, but we're passing that on to the past, which may not have actually been the case. To stick our plight onto them is unfair."

    Ann Gibbons' Science news article on the paper is also pretty helpful.

    [Terry] Hunt and co-author Carl Lipo of California State University, Long Beach, took eight samples of wood charcoal from the bottom of the oldest known archaeological site on the island, called Anakena. When they got radiocarbon dates that clustered at about 1200 C.E., Hunt at first assumed the dates were wrong and put them aside. But later he and Lipo decided to scrutinize all earlier dates from Anakena, to make sure they did not contain carbon from marine organisms or old wood, which can skew dates too old. After discarding what they considered unreliable dates, the pair found a high probability (50%) for the first human settlement starting just after 1200 C.E. The evidence does not rule out an occupation at 1000 C.E., but the probability is very low, says Hunt. The new dates are a "significant improvement" over the old ones, says radiocarbon-dating expert Tim Higham of Oxford University, U.K.

    Although several researchers welcome the rigorous analysis of dates, not everyone agrees with the criteria the team used. "Some of his criteria are fair; others are not," says zoologist David Steadman of the Florida Museum of Natural History in Gainesville, whose 1000 C.E. dates for Anakena were left in the pair's analysis.

    The new results are in keeping with a trend in the past decade toward later dates for colonization of some of the outermost Pacific islands. "This is an important paper, because it is part of a revision on the chronology of the Pacific that shows there is a big gap between settling west Polynesia [e.g., Samoa] and the marginal areas of south and east Polynesia," such as New Zealand, says archaeologist Atholl Anderson of the Australian National University in Canberra.

    And then there were the rats. From LiveScience:

    "The collapse was really a function of European disease being introduced," Lipo said. "The story that's been told about these populations going crazy and creating their own demise may just be simply an artifact of [Christian] missionaries telling stories."

    At a scientific meeting last year, Hunt presented evidence that the island's rat population spiked to 20 million from the years 1200 to 1300. Rats had no predators on the island other than humans, and they would have made quick work of the island's palm seeds. After the trees were gone, the island's rat population dropped off to a mere 1 million.

    Of course, the reason why this is a story is that it cuts against the Diamond collapse explanation.

    Thinking about it, islands just aren't very good analogies for most human societies. A group of people get to an island; there's no disease that they didn't bring with them; there are plenty of animals and plants with no natural resistance to human predation. Humans can have a pretty high intrinsic growth rate under those circumstances -- 3 kids per women can take your group from 20 to 60,000 in 400 years.

    Now what do you do? Malthusian dynamics are not our fault, especially when the rats get there first.

    References:

    Gibbons A. 2006. Dates revise Easter Island history. Science 311:1360. DOI link

    Hunt TL, Lipo CP. 2006. Late colonization of Easter Island. Science (published online) Abstract

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  • 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.

  • Paleodemographic correlates of population growth

    Sun, 2006-01-15 21:21 -- John Hawks

    Not much to do but link to this and wait for the paper to appear:

    [Jean-Pierre] Bocquet-Appel and anthropology graduate student Stephan Naji analyzed skeletal remains in 62 prehistoric North American cemeteries.

    They found that the number of immature skeletons increased by 37 percent over a 600-to-800 year period that coincides with the adoption of farming in North America about 2,500 years ago.

    ...

    The baby-boom pattern has been observed in African and European cemeteries dating about 5,000 to 7,000 years earlier, according to Bocquet-Appel. This period also coincides with the shift in those regions from foraging to agriculture at the end of the Stone Age.

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  • At least 10 percent of human genes under recent selection

    Fri, 2005-12-23 12:09 -- John Hawks

    It's hard to beat the abstract of this paper by Eric Wang and colleagues (2006):

    By using the 1.6 million single-nucleotide polymorphism (SNP) genotype data set from Perlegen Sciences [Hinds, D. A., Stuve, L. L., Nilsen, G. B., Halperin, E., Eskin, E., Ballinger, D. G., Frazer, K. A. & Cox, D. R. (2005) Science 307, 1072-1079], a probabilistic search for the landscape exhibited by positive Darwinian selection was conducted. By sorting each high-frequency allele by homozygosity, we search for the expected decay of adjacent SNP linkage disequilibrium (LD) at recently selected alleles, eliminating the need for inferring haplotype. We designate this approach the LD decay (LDD) test. By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. These results were confirmed on an independently generated data set of 1.0 million SNP genotypes (International Human Haplotype Map Phase I freeze). Simulation studies indicate that the LDD test, at the megabase scale used, effectively distinguishes selection from other causes of extensive LD, such as inversions, population bottlenecks, and admixture. The 1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function.

    Most tests of selection are blunt instruments. They depend on observations of the frequency spectrum of mutations, but mutations don't happen very often for most genetic loci. With most methods, recent selection is very difficult to find. It's like trying to find potholes when you're driving a tank -- it takes a pretty big pothole to notice anything. To find a higher proportion of the selection that happened, you need a more sensitive metric.

    The mark of a selected allele is a rapid increase in frequency. If the selection is recent, then the allele should have appear to originate recently. A rapid increase in the frequency of an allele leaves a pattern of linkage disequilibrium (LD), because recombination does not have a chance to break the selected locus apart from nearby neutral loci. The longer ago the allele increased in frequency, the more recombination and the less LD.

    Wang et al. (2006) used the prediction that the LD should decrease over time to establish a test of recent selection. They surveyed the linkage among nearby SNPs to determine whether a variant has increased rapidly in frequency during the recent past. The sensitivity of this test depends on the SNP coverage of the genome. At present, SNP coverage is very good for variants with moderate to high frequencies, so although low-frequency selected variants (those with less than a 5 - 10 percent global frequency) were missed by the current survey, it has found a huge number of selected loci.

    In conclusion, we have introduced a simple probabilistic method to detect unusual genetic architectures associated with recent selection that does not require haplotype information. It is, therefore, suitable for large chromosomal scans with large population samples. Homo sapiens have undoubtedly undergone strong recent selection for many different phenotypes, including but certainly not limited to the general categories we have defined in this work (Fig. 5). Such inferred selective events are not rare (Fig. 3). The numbers obtained, however, are similar to estimated numbers obtained for artificial selection (by humans) on the maize genome (45). Given that most of these selective events likely occurred in the last 10,000 Ð 40,000 years, a time of major population expansion out of Africa followed by regional shifts from hunterÐgatherer to agrarian societies, it is tempting to speculate that gene Ð culture interactions directly or indirectly shaped our genomic architecture (46, 47). As such, we suggest that such recently selected alleles may provide
    useful "markers" for investigating the evolutionary migrations of our species, as an adjunct to studies using neutral markers. We also propose that many of these alleles, because of their high prevalence and recent selection, should be considered likely "functional candidates" for association with human variability and the common disorders afflicting humankind.

    They also assign the loci with evidence of recent selection to different functional categories. Pathogen-host interaction loci have a high representation in the recently selected genes, as do genes related to protein and gene metabolism. And this:

    One of the more intriguing categories overrepresented in inferred selective events is neuronal function. We define this category to include a diverse assortment of genes, including the serotonin transporter (SLC6A4), glutamate and glycine receptors (GRM3, GRM1, and GLRA2), olfactor y receptors (OR4C13 and OR2B6), synapse-associated proteins (RAPSN), and a number of brain-expressed genes with largely unknown function (ASPM, RNT1; see Fig. 4).

    It would be hard for me to overstate how important this paper is. Even if it weren't central to my own current research (about which you will just have to wait for more), it brings home the vast importance of adaptive change during the most recent parts of human evolution.

    References:

    Wang ET, Kodama G, Baldi P, Moyzis RK. 2006. Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc Nat Acad Sci USA 103:135-140. Abstract

  • Diamond on skin color

    Mon, 2005-05-23 23:01 -- John Hawks

    Jared Diamond has a short review article in Nature on the evolution of skin color. This is an old story in anthropology, but it has taken some interesting twists lately with the assessment of genetic variability in some of the genes related to pigmentation. This short review covers recent papers by Nina Jablonski (2004) and George Chaplin (2004). After a short history of how skin reflectance has been measured, Diamond cuts to the selective point:

    Jablonski and Chaplin prefer a combination of two selective factors involving several costs and one benefit of UVR [ultraviolet radiation]. The costs involve the destructive photolysis of many compounds, of which Jablonski and Chaplin attach particular importance to the B vitamin folate. Everybody requires folate, so everybody would have dark skins (to screen out UVR and reduce photolysis) if there were no other selective factors. However, UVR also provides a benefit: catalysing the synthesis of vitamin D. Hence skin colour evolves as a compromise between skins light enough to permit UVR penetration for vitamin D synthesis, but dark enough to reduce folate photolysis (283).

    The folate explanation is probably the most distinctive aspect of Jablonski and Chaplin's take on skin coloration, and Diamond naturally wonders what happened to the hypothesis that skin cancer was a primary selective factor:

    Although the harmful effects of UVR are often taken to be especially associated with skin cancer, Jablonski and Chaplin minimize the importance of this aspect on the grounds of the late age of onset, after some or most of a couple's children have been morn. Most geneticists similarly minimize the selective importance of damage or disease late in life.

    Here I am sceptical. This common view may be valid for mammal species in which parent-offspring ties are severed soon after weaning, but it overlooks three of the most distinctive features of human life-histories in traditional societies: the long post-weaning dependence of offspring on parents for learning and then for social status, the large contribution of hunter-gatherer grandmothers to their grandchildren's food supply, and the dependence of an entire band or village on its oldest people as the repositories of knowledge in a preliterate society. It would be interesting to try to estimate the selective importance of skin cancers for skin-colour evolution from this perspective... (283).

    Before my reaction, it should be noted that the great importance of folate in the hypothesis of Jablonski and Chaplin is also a distinctive character of our species. Since folate is of paramount importance for normal neural growth during fetal development, the uniquely large and complex brains of humans are a greater target of selection to avoid folate photolysis.

    But Diamond's objection about skin cancer is also interesting in light of recent genomic findings concerning targets of positive selection in human evolution. Nielsen et al. (2005) (reviewed in a previous post) found that several of the genes showing the strongest evidence for positive selection in the human lineage were related to cancer risk.

    I think it likely that these genes are positively selected in order to reduce cancer risk in humans, because of our uniquely long lifespans compared to most primates, and because of the great importance of older individuals to the survival and reproduction of their younger kin. It is possible that some of these genes are particularly selected because of skin cancer itself, since the human adaptation to resist skin cancer must have been initiated as hominids lost their body fur. This time was likely substantially earlier than either any great increase in longevity or any great increase in the importance of older adults. For this reason, skin cancer risk may have been one of the earliest factors leading to selection on genes associated with tumor growth and other aspects of cancer etiology.

    Diamond also discusses exceptions to the pattern of correlation of skin color with UVR intensity:

    Of the 12 most negative residuals (skins unexpectedly dark), the highest and four others are for Bantu-speaking southern African populations that migrated from the Equator towards high southern latitudes only 2000 years ago. These populations have not yet had enough time for evolutionary loss of their equatorially adapted dark skins. Conversely, three of the nine most positive residuals (skins unexpectedly pale) are for peoples of the Philippines, Vietnam and Cambodia, who migrated towards the equator from high latitudes only in recent millennia and have not yet evolved appropriately dark skins. But why do the people of Bougainville Island in the South Pacific, and why did the Aboriginal Tasmanians, have such dark skins, after more than 10,000 years of in situ adaptation? (284)

    An answer to this question might be found in the nature of genetic alterations that lead to pigmentation levels in humans. Diamond's short review does not discuss this research, but an entrée may be found in an article on MC1R variation by Harding et al. (2000). The structure of global variation in this gene shows a relatively low level of allelic diversity in Africans and a higher level outside of Africa. The Eurasian population in particular has a high number of unrelated alleles, with many of the alleles functionally related to lighter skin tones and hair colors. The apparent pattern for this gene is a strong selective constraint within Africa for a functionally dark pigmentation, with a contrasting pattern outside Africa. This contrast may be based on a relative relaxation of selection at higher latitudes, or conversely it may reflect positive selection for many different mutations, all of which result in lighter skin color. In either case, the striking aspect of the pattern is the many ways in which skin color may be light, corresponding to the spread of several distinct mutations in the non-African human population.

    When considering small island populations, a natural hypothesis is that the necessary mutations to lighten skin color were rare enough that they may not have occurred. But the range of different mutations effectively resulting in lighter skin (if the variation of MC1R may provide a model for at least some of the genes related to skin color) tends to make me think that adaptive mutations (resulting in lighter skin) were not unlikely. For this reason, I think we must turn to the level of selection on skin color, which was either absolutely low in these populations or relatively low compared to the rate of genetic drift.

    So Diamond's question is an important one, because it essentially asks why selection upon skin color should be high in some populations and low in others. This variable nature of selection in different human populations is a venue in which we may see many more similar questions in the future.

    References:

    Chaplin G. 2004. Geographic distribution of environmental factors influencing human skin coloration. Am J Phys Anthropol 125:292-302. PubMed

    Diamond J. 2005. Geography and skin color. Nature 435:283-284. Nature online

    Harding RM et al. 2000. Evidence for variable selective pressures at MC1R. Am J Hum Genet 66:1351-1361.

    Jablonski N. 2004. The evolution of human skin and skin color. Annu Rev Anthropol 33:585-623.

    Nielsen R, et al.. 2005. A Scan for Positively Selected Genes in the Genomes of Humans and Chimpanzees. PLoS Biol 3:e170. PLoS Online

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  • The origin and evolution of the Western diet

    Thu, 2005-03-24 22:24 -- John Hawks

    There is a very nice review paper with that title in the American Journal of Clinical Nutrition, by Loren Cordain and colleagues. The basic story is in the first two sentences of the abstract:

    There is growing awareness that the profound changes in the environment (e.g., in diet and other lifestyle conditions) that becan with the introduction of agriculture and animal husbandry ~10 000 y ago occurred too recently on an evolutionary time scale for the human genome to adjust. In conjunction with the discordance between our ancient, genetically determined biology and the nutritional, cultural, and activity patterns of contemporary Western populations, many of the so-called diseases of civilization have emerged (341).

    This is far from a new story; it is what I have taught in my 100-level courses for a long time. But there are some great facts and statistics in the paper that make it a good resource.

    For example, did you know:

    Taken together, the addition of manufactured salt to the food supply and the displacement of traditional potassium-rich foods by foods introduced during the Neolithic and Industrial periods caused a 400% decline in the potassium intake while simultaneously initiating a 400% increase in sodium ingestion (350).

    Although the article introduces the issue by contrasting the putative hunter-gatherer diet with the Western diet, much of its concrete illustrations derive from the industrial revolution. The article tends to conflate these as in the above quote, and it would be worthwhile to separate these effects a bit more (although difficult because the probable degree of malnutrition and nutrient deficiency inherent in the early agricultural diet contrasts with the nutritional excesses of the Western diet.

    Here's another one:

    The typical Western diet yields a net acid load estimated to be 50 mEq/d. As a result, healthy adults consumed the standard US diet sustain a chronic, low-grade pathogenetic metabolic acidoses that worsens with age as kidney function declines. Virtually all preagricultural diets were net base yielding because of the absence of cereals and energy-dense, nutrient-poor foods -- foods that were introduced during the Neolithic and Industrial Eras and that displaced base-yielding fruit and vegetables (350).

    The main parts include a review of the advent of new foods, including dairy, cereals, refined sugars, oils, alcohol, salt, and domesticated meats, and some of the health consequences of those changes.

    References:

    Cordain L, Eaton SB, Sebastian A, Mann N, Lindeberg S, Watkins BA, O'Keefe JH, and Brand-Miller J. 2005. Origins and evolution of the Western diet: health implications for the 21st century. Am J Clin Nut 81:341-354.

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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.