Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots

The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC) existed for over two millennia (ca. 5,400–2,700 BCE) and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA) lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950–2,500 BCE)

Genetic Tracking of the Raccoon Variant of Rabies Virus in Eastern North America

AbstractTo gain insight into the incursion of the raccoon variant of rabies into the raccoon population in three Canadian provinces, a collection of 192 isolates of the raccoon rabies virus (RRV) strain was acquired from across its North American range and was genetically characterized. A 516-nucleotide segment of the non-coding region between the G and L protein open reading frames, corresponding to the most variable region of the rabies virus genome, was sequenced. This analysis identified 119 different sequences, and phylogenetic analysis of the dataset supports the documented history of RRV spread. Three distinct geographically restricted RRV lineages were identified. Lineage 1 was found in Florida, Alabama and Georgia and appears to form the ancestral lineage of the raccoon variant of rabies. Lineage 2, represented by just two isolates, was found only in Florida, while the third lineage appears broadly distributed throughout the rest of the eastern United States and eastern Canada. In New York State, two distinct spatially segregated variants were identified; the one occupying the western and northern portions of the state was responsible for an incursion of raccoon rabies into the Canadian province of Ontario. Isolates from New Brunswick and Quebec form distinct, separate clusters, consistent with their independent origins from neighboring areas of the United States. The data are consistent with localized northward incursion into these three separate areas with no evidence of east–west viral movement between the three Canadian provinces

Numerical solutions of random mean square Fisher-KPP models with advection

[EN] This paper deals with the construction of numerical stable solutions of random mean square Fisher-Kolmogorov-Petrosky-Piskunov (Fisher-KPP) models with advection. The construction of the numerical scheme is performed in two stages. Firstly, a semidiscretization technique transforms the original continuous problem into a nonlinear inhomogeneous system of random differential equations. Then, by extending to the random framework, the ideas of the exponential time differencing method, a full vector discretization of the problem addresses to a random vector difference scheme. A sample approach of the random vector difference scheme, the use of properties of Metzler matrices and the logarithmic norm allow the proof of stability of the numerical solutions in the mean square sense. In spite of the computational complexity, the results are illustrated by comparing the results with a test problem where the exact solution is known.Ministerio de Economia y Competitividad, Grant/Award Number: MTM2017-89664-PCasabán Bartual, MC.; Company Rossi, R.; Jódar Sánchez, LA. (2020). Numerical solutions of random mean square Fisher-KPP models with advection. Mathematical Methods in the Applied Sciences. 43(14):8015-8031. https://doi.org/10.1002/mma.5942S801580314314FISHER, R. A. (1937). THE WAVE OF ADVANCE OF ADVANTAGEOUS GENES. Annals of Eugenics, 7(4), 355-369. doi:10.1111/j.1469-1809.1937.tb02153.xBengfort, M., Malchow, H., & Hilker, F. M. (2016). The Fokker–Planck law of diffusion and pattern formation in heterogeneous environments. Journal of Mathematical Biology, 73(3), 683-704. doi:10.1007/s00285-016-0966-8Okubo, A., & Levin, S. A. (2001). Diffusion and Ecological Problems: Modern Perspectives. 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(2006). Asymptotic speeds of spread and traveling waves for monotone semiflows with applications. Communications on Pure and Applied Mathematics, 60(1), 1-40. doi:10.1002/cpa.20154E. Fitzgibbon, W., Parrott, M. E., & Webb, G. (1995). Diffusive epidemic models with spatial and age dependent heterogeneity. Discrete & Continuous Dynamical Systems - A, 1(1), 35-57. doi:10.3934/dcds.1995.1.35Kinezaki, N., Kawasaki, K., & Shigesada, N. (2006). Spatial dynamics of invasion in sinusoidally varying environments. Population Ecology, 48(4), 263-270. doi:10.1007/s10144-006-0263-2Jin, Y., Hilker, F. M., Steffler, P. M., & Lewis, M. A. (2014). Seasonal Invasion Dynamics in a Spatially Heterogeneous River with Fluctuating Flows. Bulletin of Mathematical Biology, 76(7), 1522-1565. doi:10.1007/s11538-014-9957-3Faou, E. (2009). Analysis of splitting methods for reaction-diffusion problems using stochastic calculus. 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Convergence analysis of one-step schemes in the method of lines. Applied Mathematics and Computation, 31, 183-196. doi:10.1016/0096-3003(89)90118-5Calvo, M. P., de Frutos, J., & Novo, J. (2001). Linearly implicit Runge–Kutta methods for advection–reaction–diffusion equations. Applied Numerical Mathematics, 37(4), 535-549. doi:10.1016/s0168-9274(00)00061-1Cox, S. M., & Matthews, P. C. (2002). Exponential Time Differencing for Stiff Systems. Journal of Computational Physics, 176(2), 430-455. doi:10.1006/jcph.2002.6995De la Hoz, F., & Vadillo, F. (2016). Numerical simulations of time-dependent partial differential equations. Journal of Computational and Applied Mathematics, 295, 175-184. doi:10.1016/j.cam.2014.10.006Company, R., Egorova, V. N., & Jódar, L. (2018). Conditional full stability of positivity-preserving finite difference scheme for diffusion–advection-reaction models. Journal of Computational and Applied Mathematics, 341, 157-168. doi:10.1016/j.cam.2018.02.031Kaczorek, T. 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Mathematical description of bacterial traveling pulses

The Keller-Segel system has been widely proposed as a model for bacterial waves driven by chemotactic processes. Current experiments on {\em E. coli} have shown precise structure of traveling pulses. We present here an alternative mathematical description of traveling pulses at a macroscopic scale. This modeling task is complemented with numerical simulations in accordance with the experimental observations. Our model is derived from an accurate kinetic description of the mesoscopic run-and-tumble process performed by bacteria. This model can account for recent experimental observations with {\em E. coli}. Qualitative agreements include the asymmetry of the pulse and transition in the collective behaviour (clustered motion versus dispersion). In addition we can capture quantitatively the main characteristics of the pulse such as the speed and the relative size of tails. This work opens several experimental and theoretical perspectives. Coefficients at the macroscopic level are derived from considerations at the cellular scale. For instance the stiffness of the signal integration process turns out to have a strong effect on collective motion. Furthermore the bottom-up scaling allows to perform preliminary mathematical analysis and write efficient numerical schemes. This model is intended as a predictive tool for the investigation of bacterial collective motion

Propagation and blocking in periodically hostile environments

We study the persistence and propagation (or blocking) phenomena for a species in periodically hostile environments. The problem is described by a reaction-diffusion equation with zero Dirichlet boundary condition. We first derive the existence of a minimal nonnegative nontrivial stationary solution and study the large-time behavior of the solution of the initial boundary value problem. To the main goal, we then study a sequence of approximated problems in the whole space with reaction terms which are with very negative growth rates outside the domain under investigation. Finally, for a given unit vector, by using the information of the minimal speeds of approximated problems, we provide a simple geometric condition for the blocking of propagation and we derive the asymptotic behavior of the approximated pulsating travelling fronts. Moreover, for the case of constant diffusion matrix, we provide two conditions for which the limit of approximated minimal speeds is positive

Massive migration from the steppe is a source for Indo-European languages in Europe

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6 . By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe

More Accurate Insight into the Incidence of Human Rabies in Developing Countries through Validated Laboratory Techniques

International audienceNo abstract availabl

A Divergent Synthetic Approach to Diverse Molecular Scaffolds: Assessment of Lead-Likeness using LLAMA, an Open-Access Computational Tool

Complementary cyclisation reactions of hex-2-ene-1,6-diamine derivatives were exploited in the synthesis of alternative molecular scaffolds. The value of the synthetic approach was analysed using LLAMA, an open-access computational tool for assessing the lead-likeness and novelty of molecular scaffolds