john hawks weblog

paleoanthropology, genetics and evolution

diet

  • Domestication, plant breeding, and micronutrients

    Sun, 2013-05-26 14:17 -- John Hawks

    An interesting essay in the New York Times today by Jo Robinson: "Breeding the Nutrition Out of Our Food". The theme is that plant domestication selected for certain traits that made our grains and vegetables more amenable to rapid calorie production, but these have often decreased the amounts of micronutrients in the resulting food products:

    Studies published within the past 15 years show that much of our produce is relatively low in phytonutrients, which are the compounds with the potential to reduce the risk of four of our modern scourges: cancer, cardiovascular disease, diabetes and dementia. The loss of these beneficial nutrients did not begin 50 or 100 years ago, as many assume. Unwittingly, we have been stripping phytonutrients from our diet since we stopped foraging for wild plants some 10,000 years ago and became farmers.

    These insights have been made possible by new technology that has allowed researchers to compare the phytonutrient content of wild plants with the produce in our supermarkets. The results are startling.

    I think it's useful to keep in mind that the qualities of food that loom important for us now, in an age of rapid transcontinental refrigerated food transportation, are not the same qualities that mattered to the first agriculturalists. Five thousand years ago, people needed food products that could be stored through the lean season, that made harvesting the plants easier, and that resisted the insults of bad weather and pathogens. Robinson focuses attention on the developments of the last hundred years, in which some crop varieties have been selected for much higher sugar content, but the long history of domestication before these recent events has also shaped the taste and nutrient content of foods.

    I also demur from the conclusion about the health of ancient people:

    Were the people who foraged for these wild foods healthier than we are today? They did not live nearly as long as we do, but growing evidence suggests that they were much less likely to die from degenerative diseases, even the minority who lived 70 years and more. The primary cause of death for most adults, according to anthropologists, was injury and infections.

    I wouldn't generalize on this point, which would be tricky to demonstrate given the evidence we have. My inclination is exactly the opposite of Robinson's implication here: the minority of hunter-gatherers who live to advanced ages are relatively healthy because the slightly less healthy ones at all life stages are more likely to be felled by infections and injury. This is the concept of "frailty" in life history theory, and is well demonstrated in some historical famines and epidemics. The people who are least healthy are least likely to survive. What we have today is an advanced ability to allow relatively unhealthy people to survive to advanced ages despite their health problems.

    Still, I think the essay's bottom line is basically correct. More diversity of foods is better. Selecting foods as part of your diet that have come from a broader array of heirloom and wild varieties is one way to add to that diversity.

    Synopsis: 
    Reacting in an essay that decries the low nutritional value of some domesticated crops
  • Weaning a Neandertal

    Sat, 2013-05-25 13:02 -- John Hawks

    Last week, Nature published a paper by Christine Austin and colleagues, in which they developed a new approach to understand how breastfeeding affects the elemental content of tooth enamel [1]. Barium and strontium are chemically similar to calcium (all three are in the same column of the periodic table of elements), and a small fraction of both elements are incorporated into enamel and dentine in place of calcium. The fractions of barium and strontium incorporated in teeth depend on an individual's diet; different food sources have different concentrations of these elements. So the concentrations of these elements in tooth enamel give some indication of the diet sources that an individual relied upon when her teeth were developing.

    Two of the most significant diet changes occur early in life -- the change at birth when an infant begins relying upon mother's milk, and the change at weaning from milk to other kinds of foods. Austin and colleagues set out to examine whether they could reliably determine the timing of these two transitions, based upon knowledge of the enamel deposition process:

    We propose that micro-spatial analysis of barium/calcium ratios (Ba/Ca) in dental tissues represents a powerful approach to assess dietary transitions. Whereas prenatal Ba transfer is restricted by the placenta, marked enrichment occurs immediately after birth from mother’s milk or infant formulas, which contain higher Ba levels than umbilical cord sera. In response to these variations in dietary Ba exposure, Ba/Ca in enamel and dentine should increase at birth, remain elevated for the duration of exclusive breastfeeding and rise further with introduction of infant formula. Circulating Ba levels are expected to change at weaning as Ba (and Ca) content and bioavailability is markedly different across plant and animal food sources. To test this hypothesis, we investigated Ba/Ca patterns in teeth from human children for whom early life diets were recorded prospectively, and in teeth from captive macaques in which maternal milk was collected and suckling behaviour observed.

    They applied their method to deciduous teeth that came from children whose mothers had participated in the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) study in Monterey County, California. This allowed Austin and colleagues to examine the fraction of barium in enamel and dentin, layer by layer, within children whose diets had been recorded including the dates of exclusive breastfeeding, supplemented breastfeeding, transition to infant formula and full weaning. The sample of teeth is not very large (only 25 individuals) but the barium signals within the teeth tracked very well with the dates reported for birth, breastfeeding and transition off milk. Additionally, Austin and colleagues considered the teeth of four macaques whose record of suckling and weaning had been recorded. The macaques did not have the confounding influence of formula supplementation, and their barium/calcium signatures gave quite clear records of natural, gradual weaning versus abrupt weaning upon the separation of mother and juvenile.

    Although both barium and strontium may provide a signal of these diet changes, Austin and colleagues focused on barium because strontium is more likely to be shifted within ancient tooth enamel after it has been buried in the ground. The goal of the paper was not only to show that the signature of breast feeding is consistent within living populations (in this case, macaques and humans) but also to provide a way to infer these dietary transitions in ancient primates. To that end, they examined the pattern within a Neandertal tooth from Scladina, Belgium:

    Chemical and temporal mapping of Neanderthal first molar enamel (Fig. 3) revealed a transition pattern similar to the macaque that weaned abruptly. After approximately 13 days of prenatal enamel formation, Ba/Ca near the enamel–dentine junction increased and remained elevated until approximately 227 days of age (~7.5 months), followed by intermediate values until 435 days of age (1.2 years). After this age Ba/Ca rapidly returned to prenatal levels for the final 1.15 years of crown formation.

    They infer that the Neandertal child was moved off exclusive breastfeeding to partial supplemented breastfeeding at around 7.5 months of age, which the authors suggest is consistent with the pattern in other primates. Then, they suggest that the extended period of breastfeeding in conjunction with solid food supplementation was "abruptly" cut off at the unusually low 1.2 years. After that time, the child continued to grow, apparently without mother's milk.

    Katie Hinde, one of the authors of the research paper, has written a blog post giving a lucid explanation of the research and its background: "Teeth and Weaning and Neanderthal… OH MY!" She discusses whether the Scladina tooth is sufficient to make inferences about Neandertal life history more generally:

    So do we think we know the species typical pattern of Neanderthal weaning? Not at all. The precipitous decrease of barium at 1.2 years of age pretty clearly suggests that the Scladina Neanderthal was abruptly weaned in a non-typical fashion.

    ...

    We have a really powerful way to investigate the period of exclusive milk feeding and the weaning process with high precision and resolution. For the first time we have a method to look at individual differences in these parameters in primates “collected” by old school naturalists gathering dust in natural history museums or skeletal material recovered at primate field sites. And we can do this in well-preserved fossil hominins... if colleagues are willing to share.

    I think this research is really great, and I was talking about it the other day as an example of how we are uncovering evidence about ancient people that was previously invisible to us. Obviously, I'd like to see the same kind of analysis extended to much larger samples of teeth. This paper is a very promising start to the research, but we need to understand what variation there may be within living humans who are eating a broader range of diets, and who may have somewhat different patterns of tooth development.

    What I think is most encouraging about this line of research is that breastfeeding may give a natural chemical tracer that will allow researchers to confirm the periodicity of enamel formation in people of known breastfeeding history. A problem in earlier research on tooth development has been the lurking possibility that the deposition process varies among people in ways that make inferences about life history and diet transitions in prehistoric humans somewhat doubtful. A more extensive record of comparative work on breastfeeding and tooth development, with large human and primate samples, has the potential to test whether between-population and within-population variation in developmental processes is important here.

    As the research develops, I keep reflecting on the plasticity of childhood development. Here we see breastfeeding as an influence upon the stable isotopes represented in teeth, but the teeth grow with or without that food source. One of the macaques showed a pulse of increased barium after being weaned entirely, which the authors suggest may have been caused by the release of barium and calcium from the skeleton and incorporation in the teeth. Our bodies use stored minerals within the skeleton as a reservoir for later biochemical needs, and acquisition of nutrients from the mother's bodily stores is an important part of that process. Human development relies upon buffers against environmental variability, and in certain physiological processes -- such as enamel formation -- we see a complex trace of those buffers interacting with extreme shifts in environmental resource availability.

    This is a really complicated way of saying that our bodies have to cope with losing people, because our ancestors lost their parents much more often than we do today. The Scladina child was part of this heritage of survival.


    References

    Synopsis: 
    A study of barium/calcium ratios in teeth shows a record of breastfeeding in a Neandertal from Scladina, Belgium
  • Paleo and "physical culture" movements

    Sat, 2013-05-04 12:01 -- John Hawks

    NPR has a short piece with an interesting historical story about old-time back-to-nature fitness fanatics: "Paleo Diet Echoes Physical Culture Movement Of Yesteryear"

    As Hamilton Stapell, a historian at the State University of New York, New Paltz, found when he went digging into the archives of physical culture, there are striking resemblances to the paleo movement today. And, he argues, this shows that people seem to romanticize a healthier past in the midst of great societal upheaval: the Industrial Revolution, in the case of physical culture; and the digital revolution, in the case of paleo.

    I don't think this specific link is very persuasive, there have been "go back to the good old days" movements since the dawn of time. Most of them have had no basis in anthropological science.

  • Oldowan hunting behaviors at Kanjera South

    Mon, 2013-04-29 16:28 -- John Hawks

    Joseph Ferraro and colleagues have done some neat analyses of the faunal remains from Kanjera South, Kenya [1]. Kanjera South is an archaeological assemblage of Oldowan artifacts and associated animal bones from around 2 million years ago. The site was once a plain next to a lake, and gradually built up clay and silt sediments over years and years of flooding and soil formation. Stone tools and bones stand out in the sediments, representing recurrent activities of ancient humans over a few hundreds or thousands of years. As a result, the site has a good statistical representation of fauna that were hunted by early humans, relatively early in the evolution of our genus.

    This is not the earliest site with evidence for meat acquisition by stone toolmakers. We know that people were butchering animals with stone tools around 2.6 million years ago. But the first really good evidence for hunting strategies is much more recent -- around 1.8 million years ago at Olduvai Gorge. There are actually very few Oldowan-era faunal assemblages large enough to study hunting behaviors. Kanjera South shows that the activities documented at Olduvai Gorge were happening a bit earlier, and the site helps to clarify the kind of context in which we might expect to find more evidence of hunting behavior.

    Hunting versus scavenging is the tiredest chestnut in anthropologists' Oldowan arsenal. Were early hunters really competent enough to bring down a duiker on their own? Or did they steal away pieces of half-eaten zebra carcases when the lions took a break?

    In reality, there is no contradiction here. Undefended meat doesn't last a day in the open, whether on the plains or near waterholes. So scavenging meat from other carnivores usually means facing them down -- not a job for an incompetent killer. Meanwhile, present-day peoples who hunt and gather rely quite a lot on "power scavenging", or taking advantage of other carnivores' successes. The present value of a dead carcass is higher than that of a live animal, as long as it may still escape you. Whether the hunter has to predict prey behavior, or the scavenger has to predict competitors' behavior, both strategies require a depth of planning. So, when it comes to Oldowan-era sites, we should expect to see a mixture of hunted and scavenged remains.

    In that context, we can make some inferences about hominin hunting practices by assessing which kinds of animals they hunted, and which they scavenged. Looking at tooth mark and cutmark evidence is not a perfect way of sorting hunting and scavenging -- because both kinds of marks are rare on faunal elements in archaeological contexts. But sometimes those comparisons lead to clear results. For example, here is the chart showing the number of tooth-marked midshaft fragments from long bones at Kanjera South, in comparison to experimental bone assemblages:

    Figure 3 from Ferraro et al 2013

    Figure 3 from Ferraro et al. 2013. Original caption: Tooth-marked mid-shaft fragments: results from experimental assemblages and excavations at KJS. Figure follows a published model [26]. Hominin-first assemblages refer to remains initially defleshed and demarrowed by hominins, then subsequently exposed to large-bodied carnivores (primarily hyenas). Carnivore-first assemblages refer to remains initially defleshed and/or demarrowed by large-bodied carnivores (primarily hyenas and/or lions). Data for body sizes 1–4 [21]. Modern data (with single standard deviations where available) derived from the literature [23]–[26], [56]–[58]. KJS frequencies are from Table 2 and Table S1. Multiple symbols for KJS indicate the results of multiple analysts. X’s indicate minimum and maximum estimates of damage (see Table S1). doi:10.1371/journal.pone.0062174.g003

    These are cool data. Carnivores who get to chew on bones for a while tend to leave the middle of them covered in tooth marks. If humans get access to the carcass early, they will strip off the meat from those midshafts, break them into bits, and otherwise prevent the taphonomic pathway to carnivore tooth marking. And in the graph we see that the Kanjera South faunal assemblage looks like cases where humans were the agents of defleshing and butchering.

    If humans had primary access to the carcasses, then the transport decisions of ancient hunters should have shaped the bone assemblage at Kanjera South. It is very common in analyses of the fauna from African Oldowan-era sites to divide the prey animals into three size classes -- small, medium and large. The majority of prey species were bovids, ranging from small antelopes to water buffalo, although most were in the small and medium size categories at Kanjera South. Ferraro and colleagues show that for medium-sized bovids, the hominins were taking two strategies. These bovids were too big to carry wholesale to a central place for sharing. So the hunters disarticulated the animals and carried back the legs, leaving the axial skeleton for the most part behind.

    Except for the heads:

    But why acquire, transport, and process an abundance of medium-sized heads? In living animals, these remains contain a wealth of fatty, calorie-packed, nutrient-rich tissues: a rare and valuable food resource in a grassland setting where alternate high-value foodstuffs (fruits, nuts, etc.) are often unavailable [2], [3], [29], [49], [52], [63], [76]–[78]. Medium-sized heads are also relatively dense and durable elements, and their internal contents are generally inaccessible to all but hyenas and tool-wielding hominins [63], [79], [80]. As a result, they are often seasonally-available as scavengable resources in East African grasslands [63], [76], [79]–[83]. Additionally, bone surface modification studies at KJS clearly demonstrate that hominins accessed internal head contents: several cranial vault and mandibular fragments bear evidence of percussion striae. Considered in sum, the presumed availability of these isolated remains across the landscape, the relative abundance of these remains in the KJS assemblages, and unambiguous material evidence that hominins exploited their contents on-site is most parsimoniously interpreted as reflecting very early archaeological evidence of a distinct hominin scavenging strategy – one that included a strong focus on acquiring and exploiting fatty, nutrient-rich, energy-dense within-head food resources (e.g., brain matter, mandibular nerve and marrow, etc.) [e.g., 24,63,76,82,84–86].

    This is John Speth's scenario for fat acquisition from lean animals. The brain is the last part of the body to become fat-depleted during times of stress. If hunters are energy-limited, further lean meat is not going to be valuable to them because protein takes energy to digest. What they need most is fat, and the most ready source of fat is the brain. Accumulation of head elements, whether from hunted or scavenged sources, is an effective behavioral strategy in those circumstances. It's one that we think Neandertals pursued at the end of winter in some parts of Europe, and a strategy followed by hunters in ethnographic and historic contexts as well.

    The paper's conclusion is well-framed as a summary of the overall value of evidence from Kanjera South.

    With regard to evolutionary ecology, the relative uniformity of hominin activities documented through the KJS sequence indicates an evolved foraging adaptation well-tuned to local ecological contexts. This point implies that hominin involvement with, and their presumed consumption of, animal remains had substantial fitness implications. In turn, sufficiently strong selective pressures are implicated as having favored the evolution of persistent hominin carnivory no later than 2.0 million years ago. This date is approximately 200,000–500,000 years earlier than previously documented [11], [20], [33], [45], and increases the known time depth of this adaptation within the hominin lineage (range of dates reflects varied interpretations of faunal materials from Olduvai [20]–[42]).

    This one was fun to read, because the data being built up at Kanjera South are really capable of testing hypotheses about hunting behavior in a way that some of the Oldovai Gorge assemblages have done up to now. Putting the faunal exploitation together with the stone tool evidence, we see a really interesting picture. As I reported a few years ago ("Plant processing with early Oldowan tools"), Kanjera South is one of the locations where we have good evidence of plant exploitation of some kind by Oldowan peoples. The site has also provided evidence about stone material transport decisions and the planning depth of stone flaking ("Technological sophistication of the earliest toolmakers". It is a good illustration of how deep knowledge of a single site, with teams returning to excavations over multiple seasons, can yield a richness of statistical information about hominin behavior.


    References

    Synopsis: 
    A faunal exploitation study finds clues about brain consumption and prey choices
  • My review of "Paleofantasy"

    Thu, 2013-03-14 16:22 -- John Hawks

    I have a review of Marlene Zuk's new book, Paleofantasy, in this week's Nature: "Evolutionary biology: Twisting the tale of human evolution" [1].

    I can't replicate my review here, but for people who have access to Nature I thought I'd bring attention to it. And if you don't have access, I wanted to share a couple of my reactions.

    It was a fun book for me to read. Zuk brings a light-hearted skepticism to a broad array of topics in human evolution. She took as her focus a collection of "paleo-advice" ideas: barefoot running, paleo diet, back-to-nature parenting advice. She then added some uncritically-accepted scientific notions about our evolution, such as the idea that agriculture was "the worst invention ever devised". To each of these topics, she brings an array of recent science questioning or disproving the assumptions. The result is not to debunk ideas, but to give a fuller (and more nuanced) perspective on how much we know (and don't know) about our evolution.

    The serious issue underlying all these topics, which Zuk recognizes, is the difficulty of reconstructing Pleistocene environments. Some hypotheses assume a fairly detailed model of ancient environments -- the so-called "environment of evolutionary adaptedness". But ancient humans lived in an array of environments, more different than each other in many ways than different parts of today's globalized world. We are unquestionably living in environments no ancient humans knew, in population size, density, disease, lifespan, and many other ways. But in other ways, our difference from some ancient people is trivial compared to their diversity. Are we well-adapted to live in cities? Perhaps not in some ways, but maybe in others.

    Probably the best part of my review to share is the end:

    As an anthropologist, I observe that Zuk's use of the term 'fantasy' is just an emphatic way of describing the hypothesis-forming that is essential to evolutionary science. We play with hypotheses, explore their predictions and try very hard to falsify them. So it is, in a way, unremarkable that so many hypotheses proposed by anthropologists about ancient environments now seem to be wrong — and, in a few cases, even ridiculous.

    It means that science is working. Genomics, high-resolution climate records, and microscopic and isotopic evidence have changed our understanding of what the past has to offer. With that in mind, let the next round of palaeofantasies begin.

    Zuk's "very brief" overview of human evolution is a lot shorter than in other recent books on the topic. I found this to be a merciful change -- how many times do I really need to read about the Australopithecus-to-humans timeline? Readers who don't already know the basic timeline are unlikely to pick up the book, I would guess. Still, if you're looking for a "latest news" about early humans, this book is not directed that way. Where it excels is its coverage of recent evolutionary changes and the shifts in Holocene environments and genetics.

    The book is not without its weak points. Without quite enough of the "paleo-advice" topics to carry the whole story, there were some real differences in tone across the chapters, with some a bit drier than others.

    People coming to this book for "the right answer" about ancient environments are not going to find it. There is no right answer, at least not a scientific one, for many of the topics covered here. Zuk has done well to talk to a range of scientists, covering these different aspects of our evolutionary history, and discuss the reasons for their disagreement.

    I wish scientists would do that for themselves more often!


    References

    Synopsis: 
    A new book by Marlene Zuk challenges some paleo advice mongers.
  • Heart disease among the ancients

    Tue, 2013-03-12 00:39 -- John Hawks

    Nicholas Bakalar covers a new paper in Lancet showing a high incidence of atherosclerosis in mummies from four ancient populations: "CT Scans Find Vascular Disease in Ancient Mummies".

    Diet and climate varied among these four groups. The Egyptians may have eaten a diet high in saturated fat. The Peruvians farmed corn, potatoes and beans, and they kept domestic animals. Ancestral Pueblans grew corn and hunted rabbits, deer and sheep, while the Aleutian Islanders subsisted on a diet of fish, shellfish, seals, sea otters and whale.

    “Patients with vascular disease feel guilty for having it, but you shouldn’t feel guilty,” Dr. Thomas said. “It’s part of the aging process. If people had it 4,000 years ago and in four different cultures, why wouldn’t we get it now?”

    The headlines around the web are saying that this study shows that a paleo diet did not protect ancient people from heart disease. Well, yeah. There's no diet that prevents heart disease. We know that pretty well by now. What I wonder is to what extent pathogens or parasites may have influenced heart disease rates in these ancient populations.

  • Coprolite microbial ecology

    Thu, 2013-02-28 00:25 -- John Hawks

    The advent of metagenomic analysis of microbial communities has led to some unexpected insights about human biology. These techniques have quietly been leading to new discoveries from old archaeological contexts. One example is Alan Cooper's work demonstrating long-term changes in oral microbiota from ancient dental calculus ("Tracing teeth troubles with fossil bacteria").

    Another is a recent paper from Cecil Lewis' lab, "Insights from characterizing extinct human gut microbiomes." [1]. The paper is open access in PLoS ONE. In it, Raul Tito and colleagues recover DNA data from ancient coprolites, from three archaeological sites in the Americas. As discussed in the paper, they obtain good data from a 1400-year-old site in Mexico. Those people, who lived near present-day Durango, were contemporaries of the classic Maya and Teotihuacanos. As such, their gut microbiomes may provide a really interesting picture of health and diet from a key period in the prehistory of the Americas.

    Coprolites may seem simple, but each represents a unique history of deposition and subsequent preservation. The microbial community may shift during the early stages of this history, and subsequent DNA damage may shift estimates of microbial abundances away from their true values. They found one of their sites appeared to preserve a good signal, while the others were degraded:

    Most striking, both Rio Zape coprolites exhibited a gut microbiome signature with similarities to the children from a rural African village with the exclusion of a sample of U.S. modern adult gut microbiomes (see Figure S4 for a heat map of these data and Figure S5 for the variability in the source proportion estimates). ZA04 also harbored similarities to non-human primate gut. The coprolites from Caserones and Hinds Cave showed little similarity to a gut microbiome environment. A portion of Caserones coprolite microbial community was similar to compost, which may be explained by the post-mortem gut serving as an organic bioreactor filled with carbon and nitrogen from decaying food detritus. The microbial community assignment for Hinds Cave failed to assign well to any source environment.

    From this, we can see that any interpretation of data from a sample of ancient coprolites must be cautious. We're generally interested in how microbial communities may have changed in ancient populations, particularly in response to other factors such as shifts in diet. But as yet it's not very clear what kinds of changes we should predict in association with diet or other changes. That makes it hard to develop a convincing test of a hypothesis.

    This paper is more of a proof of principle. And in its discussion, Tito and colleagues present different ways to explain the kinds of differences that they found in the ancient coprolite microbiota. To me, the most provocative hypothesis is that changes may have more to do with parasite load than diet:

    Information from Rio Zape also supports a current hypothesis about the composition of human microbiomes in traditional communities, potentially revealing an important aspect of the ancestral human microbiome. Spirochaetes are atypical of gut microbiomes in cosmopolitan communities. However, Treponema was reported by Filippo et al. [21] in their comparative study of modern microbiota in children from Europe and rural Africa. In their study, Treponema was observed in the rural African children but was absent in the European children. They hypothesized that the Treponema may enhance the hosts ability to extract nutrients from fibrous foods and may provide anti-inflammatory capability. They raise the hypothesis that microbiota coevolved with ancient diets and that changes in food production greatly impacted the intestinal microbiota. Treponema was also observed in the published rural data for Malawi and Venezuela [22]. The results from Rio Zape provide further support for Treponema as part of the rural human microbiome. Specifically, Treponema now is observed in four rural communities from different continents, three extant communities and one community that has been extinct for over a thousand years.

    As we uncover more comparative data from living people, we will begin to have a better picture of the covariates of microbial community structure. Today's oral bacterial populations in "cosmopolitan" post-industrial peoples are uncharacteristic of past variation. The gut microbiota of cosmopolitan peoples may be just as uncharacteristic. The diversity may have had great importance to ancient health, especially at key times when pathogens were spreading through post-agricultural populations.


    References

    Synopsis: 
    A look within the gut microbiota of ancient Americans
  • Indus curry leftovers

    Tue, 2013-01-29 21:52 -- John Hawks

    Slate has a fun story by Andrew Lawler that covers some of how we study ancient diets: "The Mystery of Curry":

    Examining the human teeth and the residue from the cooking pots, Kashyap spotted the telltale signs of turmeric and ginger, two key ingredients, even today, of a typical curry. This marked the first time researchers had found unmistakable traces of the spices in the Indus civilization. Wanting to be sure, she and Weber took to their kitchens in Vancouver, Washington. “We got traditional recipes, cooked dishes, then examined the residues to see how the structures broke down,” Weber recalls. The results matched what they had unearthed in the field. “Then we knew we had the oldest record of ginger and turmeric.” Dated to between 2500 and 2200 B.C., the finds are the first time either spice has been identified in the Indus. They also found a carbonized clove of garlic, a plant that was used in this era by cooks from Egypt to China.

    It's a nice piece. Paleoanthropologists are using similar techniques to probe the diets of Neandertals and other ancient humans. It will be a lot of fun when we can compare a wider variety of ancient cuisines.

  • Selection is for the dogs

    Wed, 2013-01-23 16:17 -- John Hawks

    I was really pleased to see the new paper by Erik Axelsson and colleagues [1] on the pattern of recent selection on domesticated dogs. As we began working on recent selection in humans, we expected that domesticated animals might exhibit similar patterns genome-wide. They are among the organisms most similar to humans in demography and ecological change: Domesticated animals have all undergone rapid shifts in diet, predator ecology and social dynamics after domestication, at the same time that they have experienced rapid increases in population size. That is a recipe for rapid adaptive evolution.

    As in humans, the paper shows that dogs were selected strongly for a new agricultural diet. Just as in humans who descend from early agriculturalists, dogs have extensive duplication of the amylase gene. Humans express amylase in saliva, but as explained in the paper dogs only produce amylase in the pancreas, where it digests starches intestinally. Where this paper gets really exciting is when the authors began to investigate the entire metabolic pathway underlying starch digestion. The amylase gene AMY2B underwent duplications similar to those in humans, and not found in wolves. Two other genes that interact in starch digestion and glucose uptake did not undergo duplication but do show near-fixed haplotypes in dogs that are absent or very rare in wolves, and the paper shows using both biochemistry and phylogenetic comparison with herbivores and omnivores that the dog versions of these genes increase enzymatic activity on starches and glucose uptake.

    In conclusion, we have presented evidence that dog domestication was accompanied by selection at three genes with key roles in starch digestion: AMY2B, MGAM and SGLT1. Our results show that adaptations that allowed the early ancestors of modern dogs to thrive on a diet rich in starch, relative to the carnivorous diet of wolves, constituted a crucial step in early dog domestication. This may suggest that a change of ecological niche could have been the driving force behind the domestication process, and that scavenging in waste dumps near the increasingly common human settlements during the dawn of the agricultural revolution may have constituted this new niche6. In light of previous results describing the timing and location of dog domestication, our findings may suggest that the development of agriculture catalysed the domestication of dogs.

    So for those of you wondering why we feed dogs kibble instead of raw beef, here's the reason.

    After finding candidate regions for selection across the genome, the authors ran a gene ontology analysis to see whether functional gene loci in these regions fall into any consistent categories. Along with the metabolic and digestive genes, they found

    The most conspicuous cluster (11 terms) relates to the term ‘nervous system development’. The eight genes belonging to this category (Supplementary Tables 7 and 8) include MBP, VWC2, SMO, TLX3, CYFIP1 and SH3GL2, of which several affect developmental signalling and synaptic strength and plasticity. We surveyed published literature and identified 11 additional CDR genes with central nervous system function (Supplementary Table 9), adding to a total of 19 CDRs that contain brain genes. These findings support the hypothesis that selection for altered behaviour was important during dog domestication and that mutations affecting developmental genes may underlie these changes7.

    That is a similar story to humans. We don't know what such genes might do, and unraveling what difference these genes may have made to behavior will take a lot of additional understanding of developmental biology. Much easier to work out what is going on when you can examine the biochemistry in vitro as with starch enzymes.

    The paper also makes clear why finding evidence of selection can be a difficult empirical problem at the moment:

    Uniquely placed sequence reads from pooled DNA representing 12 wolves of worldwide distribution and 60 dogs from 14 diverse breeds (Supplementary Table 1) covered 91.6% and 94.6%, respectively, of the 2,385 megabases (Mb) of autosomal sequence in the CanFam 2.0 genome assembly11. The aligned coverage depth was 29.8× for all dog pools combined and 6.2× for the single wolf pool (Supplementary Table 1 and Supplementary Fig. 1). We identified 3,786,655 putative single nucleotide polymorphisms (SNPs) in the combined dog and wolf data, 1,770,909 (46.8%) of which were only segregating in the dog pools, whereas 140,818 (3.7%) were private to wolves (Supplementary Table 2). Similarly we detected 506,148 short indels and 26,619 copy-number variations (CNVs) (Supplementary Files 1 and 2). We were able to experimentally validate 113 out of 114 tested SNPs (Supplementary Table 3 and Supplementary Discussion, section 1).

    If that sounds confusing, that's because it is confusing. Right now whole-genome sequencing is not yet routine, and whole-exome sequencing is not routine for creatures other than people. So maximizing the available data means working with partial genomes at varying levels of coverage, often accumulated for other purposes by other research groups using different sequencing platforms. Verifying sequence differences is not trivial. Generating a sample of gene sequences from many individuals is challenging, particularly as different individuals may be covered or not for different parts of their genomes.

    Studying selection requires a fairly large sample of genomes. This paper establishes evidence of selection on a few things in which domesticated dogs are mostly the same, and all are different from wolves. In other words, these are "complete sweeps" or "near-complete sweeps", in which a new genetic variant has become mostly fixed within the domesticated dog sample. A larger sample of dogs would be able to test selection with a broader range of strength and initial date, including "partial sweeps" and selection on standing variation that may have already existed in ancestral wolves before being subject to selection in domesticated dogs. So this paper opens a new area of inquiry on the causes of domestication without ruling out that we will discover much, much more about the history of selection in dogs.

    One really cool possibility is that we will uncover convergent or parallel patterns of selection in dogs with different geographic origins. Already we know that body size and pigmentation have been subject to selection in different dog breeds, and that single genes transferred across breeds have been important parts of that process. There are a few cases in humans where the extensive geographic dispersal of a single adaptive variant can explain the present distribution of a trait. But in many more cases, different human groups have attained traits by parallel selection on different genetic variants. Because humans control the breeding of dogs and traded dogs across long distances in historic times, we may find that dogs are much less affected by parallelism and much more by long-distance gene flow than humans. But we won't know until we put that hypothesis to the test.


    References

    Synopsis: 
    A paper finds evidence of recent selection on starch digestion in dog domestication.
  • Slow cooking Neandertal subsistence

    Tue, 2013-01-01 20:12 -- John Hawks

    During the past couple of years, new evidence has really shifted our view of Neandertal diet. Even three years ago, it was not unusual to hear Neandertals described as "hypercarnivores", more heavily reliant upon meat than any living hunter-gatherers, except possibly for Inuit who live on seal meat and whale blubber.

    The idea that Neandertals had diets with a very high fraction of meat -- maybe as high as 90-95% meat -- came from analyses of stable isotopes. I reviewed some of the stable isotope work on Neandertal diet in 2005 - "Neandertals noshed on mammoth meat?", "Neandertals: gone fishin' or not?". Here at the beginning of 2013, stable isotopes are well worth another review here on the blog.

    The extreme view of Neandertals as hypercarnivores has been softened by new evidence from several sources. Phytoliths and starch grains from Neandertal dental calculus have shown a wide variety of plants were consumed by Neandertals at least occasionally. Meanwhile, the starch grains have not only documented consumption of grains and tubers, but have also shown that Neandertals were cooking those plant foods. I wrote about the phytolith and starch granule discoveries by Amanda Henry and colleagues [1] last year ("Tartar control and Neandertal plant use").

    A new article by John Speth in Before Farming reconsiders the archaeological record of game exploitation by Neandertals and early modern humans in the Near East [2]. Speth begins with a short review of how Neandertals gradually came to be known as hypercarnivores -- in spite of many archaeologists' insistence that they must have been incompetent in various ways. After some discussion of the limits of the archaeological record, he notes that the zooarchaeological record doesn't tell us about the quantitative contribution of meat to the diet. In short:

    Lots of gazelle bones doesn’t necessarily mean lots of gazelle meat per capita per day.

    He illustrates this point with a historical case, the excavation of trash heaps from Fort Ligonier, Pennsylvania, occupied by the British during the French and Indian War. There, the total meat yield represented by animal bones was estimated at only 4,000 pounds, a tiny fraction of the meat ration known to have been issued to soldiers. The point of the example is that many biases prevent the accumulation and discovery of animal bone, even in historic contexts. The Paleolithic record of faunal exploitation can represent only the merest fraction of animal carcasses that were actually handled or consumed by ancient peoples. Biases guarantee that this record will be unrepresentative in ways that we may be poorly able to assess.

    Speth addresses the idea that Middle Pleistocene people consumed a very high fraction of meat by emphasizing that a diet of lean meat is unsustainable at such a level. If Neandertals' animal consumption was as high as Inuit peoples, then they must have been eating a high fraction of fat somehow:

    The Inuit or Eskimos provide a classic example of peoples whose traditional sustenance was provided almost entirely by meat, the diet commonly envisioned for cold-climate Neanderthals. But when looked at quantitatively, Inuit diet was actually composed primarily of fat, not lean meat, with the protein contribution seldom surpassing about 35 per cent of their calories, and usually lower, closer to 25 per cent. Pemmican, the traditional mainstay of Native Americans and First Nation peoples (‘Indians’) inhabiting the Great Plains of mid-continental North America, was a mixture of rendered fat and dried, pulverized lean meat, the mix carefully prepared so that the pro- tein component did not exceed 25–30 per cent of total energy (eg, Stefansson 1956; Speth 2010). In habitats where plant foods are neither abundant nor available for long periods of the year, and particularly for foragers in such habitats who do not store foods, fat becomes the principal non-protein macronutrient for much of the year. Foragers in the northern latitudes did obtain some carbohydrates by consuming fermented stomach contents of reindeer and ptarmigan, and sometimes inner bark (cambium), as well as small quantities of berries during the summer months (Eidlitz 1969; Gottesfeld 1992; Östlund et al 2009; Sandgathe & Hayden 2003; Zackrisson et al 2000). Until fairly recently, stomach contents were actually considered a delicacy (often referred to as ‘Eskimo ice cream’), not an emergency resource resorted to only when all else failed (Starks 2007; Speth 2010). Unfortunately, we lack quantitative data on the actual amounts that were consumed, how those amounts varied over the year, and whether men and women had comparable access. Did Neanderthals also con- sume fermented stomach contents? If so, would such a practice have had any detectable impact on their unusually high nitrogen isotope values?

    Through the middle of the article, Speth provides a detailed account of the biases due to taphonomy and ancient behavior that apply to faunal collections in Middle Paleolithic contexts. Many of these factors, such as biases in transport of different size animals, are well-known to archaeologists, but Speth's review will be useful for those who may not have studied the issue. The value of this part of the article is in its application of prey transport and landscape use to the unique geography of the Near East. Here, Middle Paleolithic peoples hunted amid water scarcity and temperature regimes that were very different from those found in Southwestern Europe. Yet by several indicators, the Middle Paleolithic population in both areas was relatively dense and successful.

    Speth reminds us that ancient hunters were active agents who made choices in their hunting strategies. Some of those choices may have been influenced by landscape use and prey abundance, but others are less easily predictable in such terms:

    The Hadza, one of the most thoroughly documented modern foraging populations, offer another interesting example. Wildebeest are one of the most abundant prey available to Hadza hunters, but they commonly avoid wildebeest in favour of zebras. Why? According to Hadza informants, the fat from wildebeest is hard and sticks to one’s teeth and palate,while zebra marrow and back-fat, especially the yellow subcutaneous deposits near the rump, are far more desirable (Oliver 1993:217; Selous 1907:220; Speth 2010:66–70). Were we to assume that Hadza hunters took prey in direct proportion to their availability on the landscape, our conclusions would be very wide of the mark.

    Back to the problem of lean meat: Hunter-gatherers in ethnographic and historical records have used boiling to degrease bone. This allows the use of the fat from inside the cancellous structure of the bone, which is a key resource supporting the use of lean wild animal meat. Boiling or slow-cooking using heated stones has been applied by many peoples around the world, and tends to leave a very distinctive archaeological trace -- the heated rocks, lined pits dug to enclose the slow-cooking mass, all show up in the archaeology. These techniques were not used by Middle Paleolithic people, or if such people used heated rocks, they did not use them terribly extensively. Stone boiling became common only later in the Upper Paleolithic of Europe.

    But Speth discusses other means of boiling, including the use of skin and bark containers. These are expedient and perishable, yet filled with water will effectively contain boiling liquid over hot coals or indirect flame. Whether such techniques were used by Neandertals remains speculative. The suggestion is latent in the identification of cooked starches within Neandertal dental calculus. If they were capable of cooking grains in moist heat, they must at least have been using bark packets or some other style of slow-cooking. The rendering of fat from bone by boiling in perishable containers would not take much additional innovation, and would have been energetically and nutritionally very advantageous.

    As I was discussing this with friends a couple of weeks ago, it occurred to me that the combination of cooked grains and meats within an animal bladder is a recurrent feature of the cuisine of Northern Europe. Neandertal haggis.


    References

    Synopsis: 
    An article about Middle Paleolithic subsistence brings a focus on meat acquisition

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