Spotted on the forest path I regularly walk the dogs along. I am assuming this poor little fish was dropped by a bird that had fished it out of the nearby Charles River. I did not check for any marks that might have confirmed that suspicion. Just goes to show that accumulating agents and site formation processes can be pretty complex.
TREE has an article in press looking at the impact of founder events on subsequent patterns of genetic diversity. The main argument of the paper, co-authored by Waters, Fraser & Hewitt (Founder takes all: density-dependent processes structure biodiversity), is that density-dependent effects associated with primary colonization/replacement events play a major role in shaping patterns of population variation. Founder effects lead to clusters of differently homogenous populations depending on which genetic variants arrived first and had initial success.
When a species encounters new opportunities, such as through colonization of new islands, colonization of recently deglaciated areas, or the extinction of a sister lineage, density-dependent processes often become particularly important and can leave long-lasting genetic signatures [5]. Although several different terms have been proposed to explain such density-dependent phenomena (e.g., leading edge, high-density blocking, and gene surfing; Figure 1), we contend that these are all largely similar and interlinked. Despite their importance for studies of gene spread, phylogeography, competitive exclusion, and biogeography, the potential biological and biogeographic restrictions imposed by density-dependent processes have often been overlooked in the scientific literature. Such an oversight may result from the focus of many researchers on ‘what has happened?’ rather than ‘what hasn’t happened?’ in ecology and evolution.
What caught my attention is that one of the examples they use in support of their argument is the “Out of Africa” expansion of modern humans. I find this a strange example for the case they are making, not because it undermines it exactly, but because it points out the tremendous complexity that can go into replacement/founder events. The authors’ argument is that initial colonizers leave lasting genetic signals because, via effects correlated with density, they are able to exclude other potential genetic variants. Applied to humans, there are a number of potential expectations you might draw, none of which provide an obvious “founder takes all” scenario.
For example, you might argue that Neandertals are the first (kind of, sort of) human population to occupy Europe, either expanding into the continent in the Mid-Pleistocene or developing out of in situ populations within Europe during that time, and subsequently waxing and waning in frequency and range throughout glacial-interglacial cycles. In this case, you might expect living Europeans to preserve a predominately Neandertal genetic signal. But obviously we do not. Most Eurasians preserve a signal of this ancestry, just not a very large one (Yang et al., 2012).
So a second way of viewing it would be that while Neandertals were the first, they were taken advantage of and more or less completely replaced by early modern humans in the 40,000-25,000 year range. This replacement was extensive enough that we might view these new human occupants as the founding population, and genetically similar to contemporary European populations. Only they are not, at least not uniformly so (Skoglund et al. 2012).
Instead, contemporary European populations are most similar to Neolithic agricultural populations that expanded out of the Near East within the past 10,000 years (Haak et al. 2010, Balaresque et al. 2010, Fu et al. 2012). It is hard to justify this population as a “founding” population in Europe in a evolutionary/demographic sense.
These kinds of population replacement events and the demographic/genetic effects the authors of this paper describe are certainly important. But in the case of human population replacements, the reality seems more complex and more case-specific than the argument provided. I would argue that the fossil, archaeological and genetic record suggest that human population replacements (and correlated collapses) are relatively common, but the pattern of continuity and discontinuity is dependent on the exact mechanisms of collapse and pattern of replacement. The demographic pattern of glacial and interglacial Neandertals, Mesolithic hunter-gatherers, and Neolithic farmers have significant differences. Furthermore, the culturally-mediated technological modifications of the expanding populations, in each case, are also quite different, setting up different possibilities for the extent of replacement versus admixture processes.
The history of human populations is dynamic and complex. There is value in thinking about general models that allow the details of specific prehistoric population events to be teased apart, but I doubt the utility of generalized explanations of human prehistory.
*****
1. Waters, Jonathan M., Fraser, Ceridwen I., Hewitt, Godfrey M. (2012) Founder takes all: density-dependent processes structure biodiversity, Trends in Ecology & Evolution. doi: 10.1016/j.tree.2012.08.024
2. Yang, M. A., A.-S. Malaspinas, et al. (2012). “Ancient Structure in Africa Unlikely to Explain Neanderthal and Non-African Genetic Similarity.” Molecular Biology and Evolution 29(10): 2987-2995. doi:10.1093/molbev/mss117
3. Pontus Skoglund,Helena Malmström, Maanasa Raghavan, Jan Storå, Per Hall, Eske Willerslev, M. Thomas P. Gilbert, Anders Götherström, Mattias Jakobsson (2012). Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe. Science 336, 466. DOI: 10.1126/science.1216304.
4. Haak, W., O. Balanovsky, et al. (2010). “Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities.” PLoS Biol 8(11): e1000536. doi:10.1371/journal.pbio.1000536
5. Fu, Q., P. Rudan, et al. (2012). “Complete Mitochondrial Genomes Reveal Neolithic Expansion into Europe.” PLoS ONE 7(3): e32473. doi:10.1371/journal.pone.0032473
6. Balaresque, P., G. R. Bowden, et al. (2010). “A Predominantly Neolithic Origin for European Paternal Lineages.” PLoS Biol 8(1): e1000285. doi:10.1371/journal.pbio.1000285
As a paleoanthropologist with both teaching and research interests spanning an array of human evolutionary topics, one of my biggest challenges is attempting to keep up with current literature. I used to get e-mail alerts when new issues of journals came out listing their contents, but given the volume of e-mail I receive, these e-mails were typically marked as read and promptly forgotten. For about two years now I have instead been slowly adding to my list of RSS subscriptions. These RSS subscriptions operate in much the same way as the old e-mail alerts, only they come pre-organized in a system separate from my e-mail, allowing me to quickly and conveniently mark off articles of interest that I can return to when I have the time.
Each RSS feed operates a little differently, though, some come online while others go offline, and others simply become overwhelming in the volume of articles they publish. This is my current list: (Titles link to RSS feed)
Science (current issue)
Nature (advanced online publication)
Nature Genetics (current issue)
Evolution
American Journal of Physical Anthropology
Journal of Human Evolution
Current Anthropology
Proceedings of the National Academy of Sciences (early edition)
Molecular Biology and Evolution
PLOS One (Evolutionary biology)
Evolutionary Anthropology
Journal of Archaeological Research
Journal of Archaeological Sciences
Journal of Vertebrate Paleontology
International Journal of Osteoarchaeology
Quaternary International
Comptes Rendus: Paleovol
American Journal of Human Genetics (new articles)
Journal of Biomechanics (current issue)
Obviously, I only read a fraction of what comes through the pipeline. But getting it delivered to my RSS reader is much easier than going out every month and searching through table of contents. Additionally, I use RSS sites of various blogs, scientific news sources, and other sites to keep track of the discussion around new research.
What am I missing?
UPDATE:
Here are a few additions thanks to comments and suggestions:
American Anthropologist
Trends in Ecology and Evolution (TREE)
Nature Reviews: Genetics
The Anatomical Record
Current Biology
Evolution & Development
Journal of Anatomy
Journal of Experimental Zoology, part A: Ecological genetics & physiology
Journal of Experimental Zoology, part B: Ecological genetics & physiology
Journal of Oral Biology and Craniofacial Research
Biological Theory: Integrating development, evolution & cognition
International Journal of Primatology
American Journal of Primatology
Animal Behaviour
South African Journal of Science
These additions may have expanded me past the breaking point…but I’ll prune as necessary.
In my Anthropology of Food class we have spent the past two weeks talking about the technological, dietary, cultural and population health transitions from the late Paleolithic, through the origin of agriculture, to present-day industrial-scale food production, with much of the discussion focused on what constitutes “good food” and the “right” kind of food production. The conversations are fascinating because of the multitude of perspectives and approaches you can take to these questions. The conversations have also got me thinking again about evolutionary diet issues and the paleodiet.
Back in the summer I had a post on the problems with the paleodiet. One of my complaints was on the notion that there is a–emphasis on the singular–paleodiet. As Pat Shipman appropriately pointed out in the comments to a follow-up post on meat and the paleodiet, when in time is the “paleo” of paleodiet. Do we mean the tropical forest diet of our ape ancestors seven million years in the past? Do we mean the shift towards a higher proportion of high-quality food items with the transition from Australopithecus to Homo about two million years ago? Or do we mean the co-evolution of humans and domesticated food production over the past 10,000 years?
Conveniently, I picked and chose from all of these options over the weekend. After a morning run with my dogs on Sunday I had an orange (ape diet) and a bowl of cereal (agricultural human diet). Later in the day I made some pork tenderloin (Pleistocene Homo diet, pretending that domesticated pigs existed during the Pleistocene) for the family, with a side of pasta (agricultural human diet) and some grapes (ape diet) for desert. I do not think my menu was particularly unusual by American standards and was variously paleo depending on your point of view. This gets at another theme from the comments to those posts, which is what constitutes the real “paleodiet” today. Is it a high percentage of calories from lean-protein sources? Or is it the consumption of a greater fraction of unprocessed, or “natural” food items?
This is not an atheoretical issue, however. It is possible to approach the question of what we are supposed to eat from an evolutionary perspective (a related issue that I hope to get to in the near future is the question of whether we should approach this from an evolutionary perspective). The starting point for such a discussion begins by recognizing that individuals interested in optimizing their health through dietary changes are not really interested in the evolutionary question. Evolution has not operated to optimize human health. In the currency of evolution, survival to and through reproduction, health is merely a correlated threshold variable. You only need to be “healthy enough” to survive and have kids. The added benefits of being able to do that and, say, run a marathon in less than 3 hours, are likely marginal from an evolutionary perspective.
Human physiology is pretty good at “getting by,” evidenced by the broad range of environments, diets, and conditions in which humans survive and thrive today. Human cultural capabilities play a big role in adding to the plasticity of human experience. Thus, evolution will operate most effectively on aspects of diet, metabolism and related physiology on areas that directly impact reproductive health, early development and survival (Peter Ellison has a useful review of energetics and reproductive ecology in Paleoanthropology).
So if an evolutionary perspective on diet is focused on optimizing evolutionary fitness rather than human health, can we still theorize a maximally healthy evolutionary diet? This requires even further clarification of terms. Is optimal health evidenced by optimal performance (you can think of this as the cross-fit perspective), maximum longevity (the immortality perspective), or a balance of longevity and performance (the Golden Girls perspective?
Someone looking to lower their cholesterol might be aiming for a very different optima than someone looking to lose 20 pounds or someone hoping to avoid prostate cancer. In each case the “right” combination of foods is likely to vary based on the genetic/ancestral background they bring with them, the specifics of their own cultural and biological development, and the realities of their current life and activity level.
And here is where I return to one of my initial statements.
The best evolutionary advice I could provide on diet is to go with what works…Your body is a better judge of what diet is right for you than any book or diet you can buy.
Engaging evolution to achieve maximum health is co-opting a system designed for a related purpose (survival and reproduction) for a personalized result. Peak sensitivities in the adaptive landscape surrounding human diet are focused on issues only partially related to health. This means that there are likely many local optima in terms of dietary health depending on what aspects of health you seek to engage and your own individual background.
John Crandall and Deb Martin write a reply to Domínguez-Rodrigo et al. (which I commented on last week) that seems to broaden some of the points I raised. They like the diagnosis of porotic hyperostosis, but are skeptical of the specificity of the conclusions in the original paper:
In summary, we wish to re-emphasize that evidence of porotic hyperostosis in ancient remains is not unilateral evidence of a meat deficient diet. In response to the findings presented by Dominguez-Rodrigo and colleagues, we feel compelled to remind scholars of the problematic nature of the skeletal and fossil records. Paleopathology, or the study of ancient diseases and abnormal bony changes like PH, lends itself to the identification of broad community patterns in health rather than the identification of specific paucities (such as a lack of meat) and has increasingly emphasized the need to carefully qualify differential diagnoses.
After a morning soccer game for my daughter, I decided to take advantage of the Columbus Day holiday on campus by doing a little cleaning of my office. I came across two old copies of the American Journal of Physical Anthropology dating to 1926 (vol. 9, no. 4) and 1927 (vol. 10, no. 1), with many of the pages still uncut. I do not remember exactly how I came upon these two issues, but it is somewhat fascinating to go back and look at the contents, much of which is focused on questions of race and identifying the distribution of anthropological characters with respect to race. The latter issue begins with a commentary from AJPA founder, Aleš Hrdlička, on the importance of anthropology in medical instruction:
The bearing of anthropological knowledge on different branches of Medicine is so intimate and important that a first-class medical education today without the anthropological aspect of things must necessarily be incomplete and constitute a serious handicap to the graduate, which he may never be able to overcome. This fact has long been recognized in Anatomy, with the result that every prominent anatomist is also more or less an anthropologist. It is strongly appreciated in Europe, and there are already a number of outstanding medical schools in this country, such as Johns Hopkins, Harvard, Rus, and those of the University of Virginia, Western Reserve at Cleveland, Washington University at St. Louis, and Leland Stanford, where some anthropological instruction at least is given to the medical student, which is supplemented in most of these establishments by opportunities for original anthropological observations. In view of the value of such instruction and research, both practical and scientific, it is safe to predict that in the not far distant future no medical college of high standing will feel justified to go on without adding a substantial course of anthropological instruction to its curriculum. Some would do so at once, were enough anthropologists available. (emphasis added)
To be fair, Hrdlička goes on in the essay to claim a large academic terrain for Anthropology, spanning all of human biology, developmental biology and human genetics, most of which are ubiquitous parts of med school curricula. But one could probably write a similar essay today, replacing Hrdlička’s emphasis on anatomy with both evolutionary and biocultural approaches in anthropology. At least Hrdlička was right about Piltdown…
Here comes the Fall…with a photo mockup of Clifford (left) and Gracie (right) looking on:
A large group of researchers working at Olduvai Gorge, including Manuel Domínguez-Rodrigo (IDEA, Madrid), Charles Musiba (UC-Denver) and Henry Bunn (U. Wisconsin), have a paper out in PLOS One this week on evidence of porotic hyperostosis in a 1.5 million year old juvenile from Olduvai. The paper happens to coincide perfectly with the pathology unit in my Forensic Anthropology class, which is wonderful.
As might be expected, much of the paper is focused on the positive identification of porotic hyperostosis in the specimen and its specific association with anemia. The bones of the skull have a natural porosity, porosity that could easily be altered by the process of fossilization and subsequent preservation through time. The authors provide a nice case for how the specific porosity observed in OH81–situated pericranially on the parietal and expressed primarily by a loss of the outer table of cortical bone–is consistent with porotic hyperostosis (though I would like to have seen a clearer indication of the exact stratigraphic position of the specimen with respect to potential diagenetic modification).
The authors then link the observation of porotic hyperostosis specifically to megaloblastic anemia:
Together, these observations suggest that if OH 81 was still nursing at the onset of anemia, then his/her mother’s diet was deficient in animal product. Alternatively, if OH 81 was being weaned at the onset of anemia, then it was the meat component of his own diet that was inadequate. The nutritional stress caused by weaning can lead to megaloblastic anemia, which frequently, in conjunction with gastrointestinal infections, produces diploic marrow hypertrophy, resulting in the ectocranial exposure of diploic trabeculae, typical of porotic hyperostosis [2].
If their diagnosis of porotic hyperostosis is correct, this is clearly evidence of a nutritionally-stressed and/or infection-laden young child (the two tend to co-occur in more complete skeletal samples – see Mensofrth, Lovejoy, Lallo & Armelagos, 1978).
Where I get confused is when the accompanying Science Daily headline says, “Eating meat may have made us human.” I happen to be in the camp that sees the origin of Homo (or maybe Homo erectus, more specifically) as part of an ecological shift within the lineage that includes a greater utilization of animal-based fats and proteins. So I am predisposed to seeing meat as important, but it is only one part of the ecological and physiological shift observed in early Homo. I have a harder time seeing this specimen as specifically indicating that a lack of meat was the de facto cause of the poor health in OH 81. This is one of the challenges of drawing broader conclusions from pathological specimens in the paleo-record. As the authors of the PLOS paper themselves conclude:
Because fossils of very young hominin children are so rare in the early Pleistocene fossil record of East Africa, the occurrence of porotic hyperostosis on one, OH 81, suggests we have only scratched the surface in our understanding of nutrition and health in ancestral populations of the deep past.
Having just scratched the surface, it is hard to expand this observation into a broader argument. I would say that rather than indicating “meat eating made us human,” this specimen is consistent with the idea that early Homo had a nutritional childhood disease profile that potentially overlaps with recent humans, with the previous absence of evidence of this kind of pathology no longer a viable point of argumentation.
This is similar to some discussions about the edentulous skull from Dmanisi, D3444, and the possibility of human social care in the Lower Pleistocene. This was a specimen that was largely, if not entirely, edentulous for an extended period of time prior to its death. Some have suggested that this is an indication of social care, as it is hard to survive in the world without teeth to serve as primary processors of food (see here, for an example of this argument). What it really demonstrates is that the range of possible explanations includes, but does not necessitate, a human-like scenario of social care going back 1.8 million years. It is hard to argue from a sample size of one, as is the case with both OH 81 and Dmanisi 3444. In the case of Dmanisi, you have to go ~1.7 million years forward in time to find the closest equivalent specimen, a Neandertal from the French site of La Chapelle-aux-Saints. For more discussion on the case of the Dmanisi specimen, check out this old post from John Hawks on the topic.
*****
1. Domínguez-Rodrigo M, Pickering TR, Diez-Martín F, Mabulla A, Musiba C, et al. (2012) Earliest Porotic Hyperostosis on a 1.5-Million-Year-Old Hominin, Olduvai Gorge, Tanzania. PLoS ONE 7(10): e46414. doi:10.1371/journal.pone.0046414
We are in the midst of considering a curricular re-shaping of our department, and I was hoping to solicit some thoughts on the minimum size necessary to produce a four-field, undergraduate Anthropology department. Wellesley College is obviously a small, liberal arts institution and the Anthropology Department here has traditionally been small, even by peer standards. We have been expanding, however, and are hoping to continue to expand. I would be interested in getting any feedback on departmental structures at small institutions (or just small departments) and any thoughts on the minimum size for viability.
NPR (at least my local NPR affiliates) has been running a series on low-cost genomic sequencing and its potentials–good and bad–for several days now. The series has focused on a variety of issues, but has regularly come back to the question of whether or not there is something to fear in personal genomics. Here is an example from a recent story:
And even when it’s right, it could open up a Pandora’s box.
“You know, it’s a seductive thought to think, well, you know, we might as well know about stuff,” said James Evans of the University of North Carolina, Chapel Hill, and the American College of Medical Genetics.
But for most people, sequencing will be just a big waste of time and money, he said.
“We don’t just get MRIs on everybody who comes to the doctor’s office. Not only would that be ridiculously expensive and uninformative,” says Evans, “it could also lead to all kinds of false positives that would be highly problematic for those people.”
Holly Dunsworth, writing at The Mermaid’s Tale, is not impressed:
It follows the recipe. (1) Start with a headline that demonstrates controversy. (2) Present a story about science-related news (which does not require controversy to be news). (3) End it ever-so briefly and vaguely with dissent, doubt, outcry or warning.
Much of the questions raised by the NPR story I link above are questions about a lack of knowledge. We don’t know exactly what information from the genome indicates, we don’t know the exact mechanisms oftentimes by which specific genetic variants impact specific phenotypic outcomes, and we don’t know what potential negative consequences might emerge from access to new knowledge. What all these questions have in common is a lack of knowledge. The answer to them should not be to shun the pursuit of this knowledge, but instead to embrace such a pursuit. There is a lot of information about us contained within our genome, and information that is potentially useful across a host of real-world issues. As I attempted to indicate in my September Anthropology News column, we should not shy away from personal genomics because of a fear or what it might reveal about each of us as an individual.
Being open to personal genomics does not necessitate being naive about the discipline, however. One of the legitimate concerns that personal genomics brings up is the potential for it to create interactions with extreme degrees of differential knowledge. Understanding the relationship between your genome and your health is not intuitive. It requires a certain degree of knowledge to know how to even approach such information. Holly’s comments about working with personal genetic data and undergraduate students get at this point indirectly:
After last spring, where over 100 students in both Human Variation and also the introductory level Human Origins (Anthropology 201) did 23andMe, not one student got “totally freaked out.” This along with much of my experience with genotyping and undergraduates indicates that, with education and with understanding, personal genomics does not induce fear. Not coincidentally, participating in personal genomics aides in education. [emphasis added]
People feel uneasy about mechanics because there is typically a large differential in knowledge about the internal workings of a combustion engine and the surrounding vehicle between a customer and the mechanic. The same potential power dynamic exists in direct-to-consumer genetic materials. The solution to fixing your car is not to avoid the mechanic, though, but instead to provide some regulatory oversight to the industry and investigate the reputation of various mechanic outfits. Of course, you don’t need to be hearing a strange clicking sound coming from your rear when you accelerate to be curious about your personal genome.
