Human ectoparasites and the spread of plague in Europe during the Second Pandemic

Plague, caused by the bacterium Yersinia pestis, can spread through human populations by multiple transmission pathways. Today, most human plague cases are bubonic, caused by spillover of infected fleas from rodent epizootics, or pneumonic, caused by inhalation of infectious droplets. However, little is known about the historical spread of plague in Europe during the Second Pandemic (14-19th centuries), including the Black Death, which led to high mortality and recurrent epidemics for hundreds of years. Several studies have suggested that human ectoparasite vectors, such as human fleas (Pulex irritans) or body lice (Pediculus humanus humanus), caused the rapidly spreading epidemics. Here, we describe a compartmental model for plague transmission by a human ectoparasite vector. Using Bayesian inference, we found that this model fits mortality curves from nine outbreaks in Europe better than models for pneumonic or rodent transmission. Our results support that human ectoparasites were primary vectors for plague during the Second Pandemic, including the Black Death (1346-1353), ultimately challenging the assumption that plague in Europe was predominantly spread by rats

Mapping the Regional Transition to Cyclicity in Clethrionomys rufocanus: Spectral Densities and Functional Data Analysis

We study the regional transitions in dynamics of the gray-sided vole, Clethrionomys rufocanus, within Hokkaido, Japan. The data set consists of 225 time series of varying length (most from 23 to 31 years long) collected between 1962 and 1992 by the Forestry Agency of the Japanese Government. To see clearly how the periodic behavior changes geographically, we estimate the spectral density functions of the growth rates of all populations using a log-spline method. We subsequently apply functional data analysis to the estimated densities. The functional data analysis is, in this context, analogous to a principal component analysis applied to curves. We plot the results of the analysis on the map of Hokkaido, to reveal a clear transition from relatively stable populations in the southwest and west to populations undergoing 3-4 year cycles in the northeast and east. The degree of seasonality in the vegetation and the rodent demography appear to be strongest in the cyclic area. We briefly speculate that the destabilization of the rodent dynamics is linked to increased seasonal-forcing on the trophic interactions in which the gray-sided voles are involved

The effect of climatic forcing on population synchrony and genetic structuring of the Canadian lynx

The abundance of Canadian lynx follows 10-year density fluctuations across the Canadian subcontinent. These cyclic fluctuations have earlier been shown to be geographically structured into three climatic regions: the Atlantic, Continental, and Pacific zones. Recent genetic evidence revealed an essentially similar spatial structuring. Introducing a new population model, the “climate forcing of ecological and evolutionary patterns” model, we link the observed ecological and evolutionary patterns. Specifically, we demonstrate that there is greater phase synchrony within climatic zones than between them and show that external climatic forcing may act as a synchronizer. We simulated genetic drift by using data on population dynamics generated by the climate forcing of ecological and evolutionary patterns model, and we demonstrate that the observed genetic structuring can be seen as an emerging property of the spatiotemporal ecological dynamics

Supplement 1. S-Plus code used to generate Figs. 2-8 and Table 2.

<h2>File List</h2><blockquote> <p>S-Plus code:</p> <p> <a href="estimation.txt">estimation.q</a><br> <a href="testing.txt">testing.q</a><br> <a href="plotting.txt">plotting.q</a><br> </p> <p>Download all files at once: <a href="blowfly-code.zip">blowfly-code.zip</a></p> <p>All individual files are in ASCII text. The .zip file requires WinZip to extract. </p> </blockquote><h2>Description</h2>Following are the S-Plus files (in ascii format) that were used in conjunction with the time series described in the paper to generate Figs. 2-8 and Table 2. The file estimation.q contains the code to estimate all functions and parameters in the model in Eqs. 5-10. After execution the list fit.all contains estimates found on the basis of individual populations, whereas the list fit.cmb contains estimates found on the basis of combining the replicates. Note that the S-Plus code in estimation.q has to be executed before executing the other S-Plus files described below. <p> The file testing.q contains the code to generate the entries of Table 2, i.e., code for applying the Mann-Whitney <i>U</i> test and the Kolmogorov-Smirnov test to estimated parameters as described in the paper. </p><p> The file plotting.q contains the code to generate Figs. 2-8 based on the estimates found using estimation.q. </p