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UltrasSoc_cover_epub Over the past few years one of the major finds of ancient DNA is that human genetic patterns as a function of time often exhibit discontinuity. In plain language, the people who live in a given location are often unlikely to have descendants at that location 10,000 years down the line. This has resulted in an update to long held null and consensus models of of modern human dispersal across the world. To sum it up, that family of models tended to be predicated on a sequence of unidirectional migrations out of Africa in a step-wise fashion. This resulted in the stylized fact that genetic diversity decreased as a function of distance, with groups like Native Americans and Oceanians the most “steps” from Africans. Though all non-African populations are separated by the same number of generations from Africans, one result that would be implied and was seen in the data is that genetic distance from Africans of these populations was often higher than Eurasians, likely a function of their elevated drift (more drift means more divergence from ancestral shared allele frequencies). Once these regions were settled at a given time in the past genetic diversity so partitioned would slowly equilibrate through gene flow between adjacent demes.

F1.large (1) Though this model captures some element of the truth, the reality of sharp local discontinuities in a given region is strongly indicative of the fact that there was no stable state achieved once the initial founders arrived. Geographical reality seems to dictate the sort of pattern of settlement outlined by the model of serial bottleneck Out-of-Africa model, but it seems likely that future population arrivals could be drawn from both closer to, and further out, from Africa. Second, it turns that most of the world’s populations are the product of relatively recent admixtures between very different ancestral lineages. Instead of overlaying a phylogenetic tree over a spatial landscape, one has to conceive of it as a reticulate network. This revised model is outlined in Joe Pickrell and David Reich’s Towards a new history and geography of human genes informed by ancient DNA. In place of diffusion and continuous genetic exchange between adjacent demes, the empirical data seems to point to a non-trivial proportion of “pulse admixtures.” That is, people who were very genetically different arrived, and mixed in with the local population, in a very short period. Sort of what happened in the New World with the arrival of Europeans.

But that’s all talk. A new paper in Molecular Biology & Evolution formally models these processes, Long distance dispersal shaped patterns of human genetic diversity in Eurasia (open access):

…However, it is likely that the Last Glacial Maximum (LGM) affected the demography and the range of many species, including our own. Moreover, long-distance dispersal (LDD) may have been an important component of human migrations, allowing fast colonization of new territories and preserving high levels of genetic diversity. Here, we use a high-quality microsatellite dataset genotyped in 22 populations to estimate the posterior probabilities of several scenarios for the settlement of the Old World by modern humans. We considered models ranging from a simple spatial expansion to others including LDD and a LGM-induced range contraction, as well as Neolithic demographic expansions. We find that scenarios with LDD are much better supported by data than models without LDD. Nevertheless, we show evidence that LDD events to empty habitats were strongly prevented during the settlement of Eurasia. This unexpected absence of LDD ahead of the colonization wave front could have been caused by an Allee effect, either due to intrinsic causes such as an inbreeding depression built during the expansion, or to extrinsic causes such as direct competition with archaic humans. Overall, our results suggest only a relatively limited effect of the LGM-contraction on current patterns of human diversity. This is in clear contrast with the major role of LDD migrations, which have potentially contributed to the intermingled genetic structure of Eurasian populations.

One of the things the authors found is that low population pairwise genetic distances across a wide range of human populations in Eurasia is probably due to LDD events homogenizing the landscape. Continuous gene flow between demes after the initial settlement Out-of-Africa would not have resulted in these patterns. Second, it seems reading the paper that the weak effect of the LGM population reductions on genetic diversity are partly a function of this mixing across long distances. Finally, it is notable in within Eurasia at least (they suggest that the Americans and Oceania may not fit this pattern) a sort of diffusion/wave of advance model does hold for the initial arrival of modern humans in Eurasia. They posit that this might be because archaic populations prevented long distance movements, or, that population fitness became too low when the bands were too small, the reference to the allee effect. Additionally, they also note that the evidence in Europe suggests both replacement with minimal admixture, and then later admixture with the local substrate.

But the details are less important than the big picture. The authors note that there are aspects of the data (dozens of microsatellites) that leave something to be desired, but this is a first pass. At the top of this post you see Peter Turchin’s Ultrasociety. Though the authors don’t get into much specificity in the discussion, I think the solution to what’s going on, and how LDD seems prevalent when you have a populated landscape, is that cultural complexity resulted in sharply increased returns to the victors in inter-group competition. Though some of the dynamics date back to the Pleistocene, the re-patterning of the world with “LDD”, what I call “leapfrogging”, is probably most salient for Eurasia during the Holocene. And, as the story about the Yakutian horses implies, this is also relevant to many domestic lineages.

 
• Category: Science • Tags: Demography, Genetics, History 
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Citation: Lippold, Sebastian, et al. "Human paternal and maternal demographic histories: 4 insights from high-resolution Y chromosome and mtDNA sequences 5." Methods 1 (2014): 2.

Citation: Lippold, Sebastian, et al. “Human paternal and maternal demographic histories: 4 insights from high-resolution Y chromosome and mtDNA sequences 5.” Methods 1 (2014): 2.

Alexander Kim has already responded in depth to a new paper in Investigative Genetics, Human paternal and maternal demographic histories: insights from high-resolution Y chromosome and mtDNA sequences:

Results
We identified 2,228 SNPs in the NRY sequences and 2,163 SNPs in the mtDNA sequences. Our results confirm the controversial assertion that genetic differences between human populations on a global scale are bigger for the NRY than for mtDNA, although the differences are not as large as previously suggested. More importantly, we find substantial regional variation in patterns of mtDNA versus NRY variation. Model-based simulations indicate very small ancestral effective population sizes (<100) for the out-of-Africa migration as well as for many human populations. We also find that the ratio of female effective population size to male effective population size (Nf/Nm) has been greater than one throughout the history of modern humans, and has recently increased due to faster growth in Nf than Nm.

Conclusions
The NRY and mtDNA sequences provide new insights into the paternal and maternal histories of human populations, and the methods we introduce here should be widely applicable for further such studies.

Comparing male and female demographic histories can be a mug’s game. But if one is appropriately cautious some insight can be gained, and in this paper the authors are appropriately cautious. It isn’t surprising that female effective population sizes are somewhat larger over the long term and across deep history than male ones for our lineage. We’re a mildly sexually dimorphic species, suggestive of possible mild polygyny at best, on average. In other words, males compete, but not that much. Far more interesting to me is what Alexander Kim keys in on:

Among the most interesting inferences is Holocene crash in male Ne, with no clear reflection on the mitochondrial side of things, everywhere but Oceania and America — most dramatically in the Middle East/North Africa:

Not from the Pleistocene

Not from the Pleistocene

As a speculative matter this might reflect the rise of “super-male” lineages that arose with agriculture and mass society. In other words, extreme levels of polygyny are a novel cultural evolution, which could only emerge with the level of stratification and power accumulation in patrilineages enabled by agricultural, or agro-pastoral, societies. Hyper-polgyny might also be correlated with the extreme mate guarding and sexual jealousy which is the norm among many Eurasian societies. The implication here is that many of the “regressive” social practices we associate with “traditional” Eurasian societies are simply cultural retrofits to adapt to new social circumstances enabled by mass society. Liberal individualism as an ethos may not be a novel innovation, as much as the emergence of long submerged instincts which evolved when collective institutions and interests were far weaker as forces in our day to day decision making.

 
• Category: Science • Tags: Demography 
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One of the assumptions that I’ve made on this weblog repeatedly based on ancient literary references is the idea that before 1900 urban areas were population sinks. In Blessed Among Nations: How the World Made America the historian Eric Rauchway asserts that ~1900 in the USA urban health and life expectancy surpassed that of rural areas, arguably a first in the history of the world (the reason for this was a public health revolution prompted by fear of the diseases which Southern and Eastern European immigrants were presumably bringing to American cities). It’s not that difficult to find data on early modern urban areas, which does confirm the lower fertility vis-a-vis rural areas, and often an excess of deaths over births (some scholars have argued that this second is an artifact of the transient nature of urban residency for a large segment of the population). Most of the older research seems based on extrapolation from archaeology and physical anthropology. But I did find one paper from 1913 which looked at inscriptions on tombstones in the Roman Empire to calculate curves of life expectancy at a given time from three locations: Rome, the Iberian provinces, and Roman North Africa. The first was an urban location, and the latter two less urban ones.

The paper is ON THE EXPECTATION OF LIFE IN ANCIENT ROME, AND IN THE PROVINCES OF HISPANIA AND LUSITANIA, AND AFRICA.

Some caveats:

- The author notes than underrepresentation of lower status individuals in marked graves. This is expected. But, one presumes that life expectancy curves calculated from slaves and urban proletarian would probably be very different from what you see below. Days of birth and death listed on a tombstones indicates a level of functional literacy in the class from which the individual is derived (even if the individual was an illiterate, their family and friends are likely to have included literates).

- Some of the ages at death recorded are almost certainly fictitious exaggerations. I don’t think the author expresses proper skepticism of recorded ages in ancient Rome.

- All that being said, the key is to focus on differences between locations. Unless there are systematic biases which vary by location (e.g., more marked graves among lower status individuals in urban Rome) we’re getting a sense of differences of mortality. As a reference the author naturally uses the English of circa 1900.

The charts are in order those of Rome, the two Iberian provinces, and Africa.


romelife

spanlife

aflife

What you see on the x-axis are ages of individuals, and on the y-axis the expected years of life at that age. The lower life expectancy for women at all ages in the ancient world except for among the very old is in line with our intuitions. In a pre-modern environment there was no necessary expectation of “women and children first” in times of want, and women had to bear offspring which would be a net drain on their resources. Older women do not bear as many of these costs. At least the one of having to bear offspring. The author explains the higher life expectancy of older individuals in the Rome Empire as being due to a process of selection; the healthiest made it to more advanced ages. This sounds plausible, but I suspect part of it also has to do with inflation of ages for those who make it do an advanced age. Finally, you see the noticeable difference between Rome and the provinces. The author sees this as confirmation of the contemporary literary sources which point to the lack of healthfulness of ancient urban life. He also adds an addendum that after the paper was drafted a correspondent pointed him to another analysis which included a Gallic sample, which confirmed again that provincials seemed to have a higher life expectancy.

I don’t think that our argument can hinge on this one analysis, and I’ll be digging further. To get a better sense though of ancient Roman urban areas soon I’ll look to see what there is on Alexandria, since Egypt is one area because of climate that ancient documents have been preserved. It’s interesting that this idea that cities are demographic sinks seems widely accepted in the literature, but there’s been little cliometric exploration of the ancient data…though who can blame them given the nature of the ancient textual records.

(Republished from Discover/GNXP by permission of author or representative)
 
• Category: History, Science • Tags: Demography, Urbanization 
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Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at http://www.razib.com"