Razib Khan One-stop-shopping for all of my content

September 23, 2010

The city that kills you makes you strong!

ResearchBlogging.orgOver the past day I’ve seen reports in the media of a new paper which claims that long-term urbanization in a region is strongly correlated with genetic variants for disease resistance. I managed to find the paper on Evolution’s website as an accepted manuscript, ANCIENT URBANISATION PREDICTS GENETIC RESISTANCE TO TUBERCULOSIS:

A link between urban living and disease is seen in recent and historical records, but the presence of this association in prehistory has been difficult to assess. If the transition to urbanisation does result in an increase in disease-based mortality, we might expect to see evidence of increased disease resistance in longer-term urbanised populations, as the result of natural selection. To test this, we determined the frequency of an allele (SLC11A1 1729 + 55del4) associated with natural resistance to intra-cellular pathogens such as tuberculosis and leprosy. We found a highly significantly correlation with duration of urban settlement – populations with a long history of living in towns are better adapted to resisting these infections. This correlation remains strong when we correct for auto-correlation in allele frequencies due to shared population history. Our results therefore support the interpretation that infectious disease loads became an increasingly important cause of human mortality after the advent of urbanisation, highlighting the importance of population density in determining human health and the genetic structure of human populations.

298px-Pericles_Pio-Clementino_Inv269In some ways this seems plausible. There are a priori reasons why we’d expect to see a great deal of evolutionary change in regions of the genome correlated with variations in immune response. Diseases are one of the most likely reasons for why sex exists in complex multicellular species; sex allows a slow-reproducing population to bend with the rapid-fire punches of their pathogens by shuffling their defenses constantly. The results from recent work mapping patterns of variation in relation to natural selection generally indicate that immune related regions show plenty of signs of adaptation. No surprise, a “Red Queen” model whereby pathogens and their hosts constantly co-evolve would imply that immunologically relevant genes would never be at equilibrium frequencies for long, so we’d have a good shot at catching “selective sweeps” on some of the immune loci.

So how do cities play into this picture? I suspect that the picture is more complicated than the presentation in the paper, though I believe that the authors were constrained by considerations of space from evaluating all possibilities in full depth. There are two facts which I think are critical to understanding the pattern of variation here:


- All pre-modern societies were predominantly rural demographically. The difference between an “urban civilization” like Rome and a non-urban one such as Dark Age Ireland was that ~25% of the residents of the Roman Empire lived in urban areas (generously defined) while ~0% of Dark Age Irish lived in urban areas. Rome is generally considered to be a very urban pre-modern society, perhaps the most urban large-scale society before the 17th century.

- I also believe that ancient cities were population sinks. People simply did not replace themselves and cities only perpetuated their massive scale by serving as magnets for excess population from the rural hinterlands. Without appropriate political structures to maintain the population and generate incentives for an inflow migration ancient cities withered away very fast (Rome’s population went from hundreds of thousands to tens to of thousands in the 100 years from the early 6th to early 7th century because of political instability).

Before I go on much, let’s address the results presented in the paper. Below you see the frequencies of the allele which is more protective against tuberculosis in tabular form and on a map, as well as the logistic regressions which show the relationship between time since urbanization and the allele frequencies. Please note that they corrected for genetic relatedness in their regression, so the correlation isn’t just due to population stratification on a world wide scale.

Since the allele which confers resistance is at a high frequency everywhere the difference is between those populations where the genotypes are predominantly in a homozygote state (e.g., Iranians), and those where only around half are resistant homozygotes (e.g., Sami). The authors note that because of the high frequency everywhere, including populations with no history of agriculture such as the Sami, one can’t posit a model where positive selection drove the disease resistant alleles from 0 to fixation. Rather, it perturbed the equilibrium frequency. Using the Tajima’s D statistic they do find evidence of balancing selection in both East Asians and Europeans. This would be in keeping with frequency-dependent models of pathogen-host co-evolution.

As I said before there are strong reasons to assume that natural selection reshaped the genomes of populations over the past 10,000 years. It really isn’t if, it’s how and what. The authors present some evidence for a particular variant of the gene SLC11A1 being the target of natural selection. To really accept this specific case I think we’ll need some follow up research. Rather, I want to focus on the narrative which is being pushed in the media that cities were the adaptive environments which really drove the shift in allele frequencies. I don’t think this was the case, I think the cities were essential, but I don’t think ancient urbanites left many descendants. Instead, I think cities, or urbanization, is first and foremost a critical gauge of population density and social complexity. Second, I believe that cities serve as facilitators and incubators for plague. In other words both urbanization and disease adaptation are derived from greater population density, while urbanization also serves a catalytic role in the spread of disease. This could explain the strong correlation we see.

I believe that the Eurasians who may have been subject to natural selection due to the rise of infectious disease are almost all the descendants by and large of ancient rural peasants, or, their rentier elites. These peasants were subject to much greater disease stress even without living in urban areas than hunter-gatherers and pastoralists because their population densities were higher, and quite often they were living a greater proportion of their lives snuggly against the Malthusian lid. Hunter-gatherers may have been healthier on average because of a more diversified diet as well as lower population densities due to endemic warfare. In contrast, agriculturalists lived closely packed together and were far more numerous than hunter-gatherers, and, their immune systems were probably less robust because of the shift away from a mix of meat, nuts and vegetables, to mostly grains.

800px-Republik_Venedig_Handelswege01A downstream consequence of agriculture was the rise of cities through the intermediate result of much higher population densities. I accept the literary depiction of ancient cities as filthy and unhealthful. There’s almost certainly a reason that pre-modern elites idealized rustic life, and had country villas. Additionally, though I assume that both the rural peasantry and urban proletarian led miserable lives, I believe that in terms of reproductive fitness the former were superior to the latter. From what I have read city life only became healthier than rural life in the United States in 1900, in large part due to a massive public health campaign triggered by fear of immigrant contagion. The high mortality rates and low reproductive fitness of urbanites implies that evolutionarily the more important role of cities were as nexus points for trade and the spread of disease. The book Justinian’s Flea chronicles the pandemic in the Roman Empire in the 6th century, in particular its origin in Constantinople from points east. We’re well aware today that a globalized world means that there’s an interconnectedness which can bring us strength through comparative advantage, but also catastrophe through contagion. This is a general dynamic, not simply one applicable to disease, but in the world before modern medicine the utility of trade networks for pathogens would have been of great importance.

One can imagine societies through the organismic lens as if they were cyclical wind-up toys. In the initial stage of expansion and integration political stability and concentration of power results in a peace which allows for the increase in population as more land inputs are thrown into primary production. Eventually diminishing returns kicks in and there’s no more land, so the labor squeezes itself more tightly on fixed land endowments. Their median physiological fitness declines as the pie gets cut into more and more pieces. All the while these massive numbers of peasants serve as the source of revenue for extractive elites, who found and patronize cities where they can signal their status and concentrate their wealth. Most pre-modern cities, like Rome and Constantinople, would have been economic parasites, depending on rents and plunder. As a sidelight cities such as Constantinople which were placed at transportation hubs would also become the focal points for trade, especially if they could be termini themselves for the luxury good trade which was dependent on the demand from rentier elites in residence in the metropolis. Finally, these cities would also be magnets for masses of armies because of the inevitably of sieges.

400px-Plato_Silanion_Musei_Capitolini_MC1377Eventually the combination of factors would result in the outbreak of plague. Social order would collapse, people would flee the cities, and populations would drop as the tightly run ship on the Malthusian margin ran aground. As the population dropped median health and wealth would return, and susceptibility to plague would decrease. And then the cycle of expansion and integration would start anew.

This is I believe the story of the rise and fall of urban societies which reshaped the genomes of people who lived across much of Eurasia. It isn’t a tale of urbanites, rather, urbanites for most of history have almost certainly been epiphenomena in a genetic sense. They’re the excess rural population which finds its way to the polis. Because of the squalor and lack of public health the lot of the urbanite was to consign their genes to oblivion. But for this deal with the devil the urban man had an opportunity to become immortal, and live on in human memory. It is their names which echo down through history, and roll off the tongues of the descendants of the peasants who have long ago forgotten their own genetic forebears.

Citation: Barnes, I., Duda, A., Pybus, O., & Thomas, M. G. (2010). ANCIENT URBANISATION PREDICTS GENETIC RESISTANCE TO TUBERCULOSI Evolution : 10.1111/j.1558-5646.2010.01132.x

Image Credit: Marie-Lan Nguyen, Nikater

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