Improved Complexity Bounds for Counting Points on Hyperelliptic Curves

We present a probabilistic Las Vegas algorithm for computing the local zeta function of a hyperelliptic curve of genus $g$ defined over $\mathbb{F}_q$. It is based on the approaches by Schoof and Pila combined with a modeling of the $\ell$-torsion by structured polynomial systems. Our main result improves on previously known complexity bounds by showing that there exists a constant $c>0$ such that, for any fixed $g$, this algorithm has expected time and space complexity $O((\log q)^{cg})$ as $q$ grows and the characteristic is large enough.Comment: To appear in Foundations of Computational Mathematic

Reconceptualising evolution by natural selection

This thesis examines the theoretical and philosophical underpinnings of the concept of natural selection which is pervasively invoked in biology and other ‘evolutionary’ domains. Although what constitutes the process of natural selection appears to be very intuitive (natural selection results from entities exhibiting differences in fitness in a population), this conceals a number of theoretical ambiguities and difficulties. Some of these have been pointed out numerous times; others have hardly been noticed. One aim of this work is to unpack these difficulties and ambiguities; another is to provide new solutions and clarifications to them using a range of philosophical and conceptual tools. The result is a concept of natural selection stripped down from its biological specificities. I start by revisiting the entangled debates over whether natural selection is a cause of evolutionary change as opposed to a mere statistical effect of other causes, at what level this putative cause operates and whether it can be distinguished from drift. Borrowing tools from the causal modelling literature, I argue that natural selection is best conceived as a causal process resulting from individual level differences in a population. I then move to the question of whether the process of natural selection requires perfect transmission of types. I show that this question is ambiguous and can find different answers. From there, I distinguish the process of natural selection from some of its possible products, namely, evolution by natural selection and complex adaptation. I argue that reproduction and inheritance are conceptually distinct from natural selection, and using individual-based models, I demonstrate that they can be conceived as evolutionary products of it. This ultimately leads me to generalise the concepts of heritability and fitness used in the formal equations of evolutionary change. Finally, I argue that concepts of fitness and natural selection crucially depend on the grains of description at and temporal scales over which evolutionary explanations are given. These considerations reveal that the metaphysical status of the process of natural selection is problematic and why neglecting them can lead to flawed arguments in the levels of selection debate

Reconceptualising evolution by natural selection

This thesis examines the theoretical and philosophical underpinnings of the concept of natural selection which is pervasively invoked in biology and other ‘evolutionary’ domains. Although what constitutes the process of natural selection appears to be very intuitive (natural selection results from entities exhibiting differences in fitness in a population), this conceals a number of theoretical ambiguities and difficulties. Some of these have been pointed out numerous times; others have hardly been noticed. One aim of this work is to unpack these difficulties and ambiguities; another is to provide new solutions and clarifications to them using a range of philosophical and conceptual tools. The result is a concept of natural selection stripped down from its biological specificities. I start by revisiting the entangled debates over whether natural selection is a cause of evolutionary change as opposed to a mere statistical effect of other causes, at what level this putative cause operates and whether it can be distinguished from drift. Borrowing tools from the causal modelling literature, I argue that natural selection is best conceived as a causal process resulting from individual level differences in a population. I then move to the question of whether the process of natural selection requires perfect transmission of types. I show that this question is ambiguous and can find different answers. From there, I distinguish the process of natural selection from some of its possible products, namely, evolution by natural selection and complex adaptation. I argue that reproduction and inheritance are conceptually distinct from natural selection, and using individual-based models, I demonstrate that they can be conceived as evolutionary products of it. This ultimately leads me to generalise the concepts of heritability and fitness used in the formal equations of evolutionary change. Finally, I argue that concepts of fitness and natural selection crucially depend on the grains of description at and temporal scales over which evolutionary explanations are given. These considerations reveal that the metaphysical status of the process of natural selection is problematic and why neglecting them can lead to flawed arguments in the levels of selection debate

Counting points on genus-3 hyperelliptic curves with explicit real multiplication

We propose a Las Vegas probabilistic algorithm to compute the zeta function of a genus-3 hyperelliptic curve defined over a finite field $\mathbb F_q$, with explicit real multiplication by an order $\mathbb Z[\eta]$ in a totally real cubic field. Our main result states that this algorithm requires an expected number of $\widetilde O((\log q)^6)$ bit-operations, where the constant in the $\widetilde O()$ depends on the ring $\mathbb Z[\eta]$ and on the degrees of polynomials representing the endomorphism $\eta$. As a proof-of-concept, we compute the zeta function of a curve defined over a 64-bit prime field, with explicit real multiplication by $\mathbb Z[2\cos(2\pi/7)]$.Comment: Proceedings of the ANTS-XIII conference (Thirteenth Algorithmic Number Theory Symposium

Navigocorpus: A Database for Shipping Information - A Methodological and Technical Introduction

International audienceNavigocorpus is a database which stores information about shipping information from the XVIth century on. Each travel is stored as a list of chronologically ordered points (ports and high-sea points). Any kind of information items (taxes paid, cargo items loaded and unloaded, commercial operations, sea hazards, characterization of the point or of the ship, etc.) can be linked to any point. The result is a highly flexible and powerful tool. Any kind of extra information can be inserted at any moment, from original sources or existing databases. Navigocorpus is based on FileMaker. Any kind of data processing is allowed. It was elaborated as part of a French ANR research project, and is based on FileMaker.Navigocorpus est un système de bases de données qui recueille des informations relatives aux mouvements de navires à partir du XVIe siècle. Chaque voyage de chaque navire est stocké sous la forme d'une suite de points rangés par ordre chronologique. A chaque point, tout type d'information peut être lié (cargaisons, caractéristiques du point ou de l'étape, opérations commerciales, taxes versées, intervention de tout acteur, événements de mer, etc.). Il en résulte un instrument très puissant, qui permet tout type de traitement et surtout l'insertion, à tout instant, de toute donnée provenant de sources originales ou d'autres bases de données. Navigocorpus a été développé dans le cadre de l'ANR du même nom, sous FileMaker

3' RNA ligase mediated rapid amplification of cDNA ends for validating viroid induced cleavage at the 3' extremity of the host mRNA

Abstract : 5′ RNA ligase-mediated rapid amplification of cDNA ends (5′ RLM-RACE) is a widely-accepted method for the validation of direct cleavage of a target gene by a microRNA (miRNA) and viroid-derived small RNA (vd-sRNA). However, thi\s method cannot be used if cleavage takes place in the 3′ extremity of the target RNA, as this gives insufficient sequence length to design nested PCR primers for 5′ RLM RACE. To overcome this hurdle, we have developed 3′ RNA ligase-mediated rapid amplification of cDNA ends (3′ RLM RACE). In this method, an oligonucleotide adapter having 5′ adenylated and 3′ blocked is ligated to the 3′ end of the cleaved RNA followed by PCR amplification using gene specific primers. In other words, in 3′ RLM RACE, 3′ end is mapped using 5′ fragment instead of small 3′ fragment. The method developed here was verified by examining the bioinformatics predicted and parallel analysis of RNA ends (PARE) proved cleavage sites of chloride channel protein CLC-b-like mRNA in Potato spindle tuber viroid infected tomato plants. The 3′ RLM RACE developed in this study has the potential to validate the miRNA and vd-sRNA mediated cleavage of mRNAs at its 3′ untranslated region (3′ UTR)

An harmonious encoding of instrument values by a 19th century Parisian violin dealer

International audienceThe study of three ledgers from the archives of a prominent Parisian violin maker's workshop (active from 1796 to 1948) reveals that some of their content was encrypted. We present here the deciphering of the code, and a discussion of its use in the context of the workshop. Charles-Adolphe Gand introduced this code around 1847 to encrypt values of antique/used violins he would buy and resell. His successors maintained the use of this code at least until 1921. Taking a few examples of instruments by Stradivari and other violin makers, we illustrate how the decoded ledgers –listing transactions for more than 2,500 instruments– are of high interest as historical sources documenting the margins, rebates, and commercial practices of these violin dealers. More generally, will contribute to better describing the evolution of the market for antique instruments of the violin family

Experimental infection of Pacific oyster Crassostrea gigas spat by ostreid herpesvirus 1: demonstration of oyster spat susceptibility

In 2008 and 2009, acute mortalities occurred in France among Pacific cupped oyster, Crassostrea gigas, spat. Different hypothesis including the implication of environmental factors, toxic algae and/or pathogens have been explored. Diagnostic tests indicated that OsHV-1 including a particular genotype, termed OsHV-1 μVar, was detected in most of samples and especially in moribund oysters with the highlighting of virus particles looking like herpes viruses by TEM examination. In this study, an experimental protocol to reproduce OsHV-1 infection in laboratory conditions was developed. This protocol was based on the intramuscular injection of filtered (0.22 μm) tissue homogenates prepared from naturally OsHV-1 infected spat collected on French coasts during mortality outbreaks in 2008. Results of the experimental trials showed that mortalities were induced after injection. Moreover, filtered tissue homogenates induced mortalities whereas the same tissue homogenates exposed to an ultraviolet (UV) treatment did not induce any mortality suggesting that oyster spat mortalities require the presence of a UV sensitive agent. Furthermore, analysis of injected oyster spat revealed the detection of high amounts of OsHV-1 DNA by real-time quantitative PCR. Finally, TEM analysis demonstrated the presence of herpes virus particles. The developed protocol allowed to maintain sources of infective virus which can be useful for the development of further studies concerning the transmission and the development of OsHV-1 infection

Wolbachia Age-Sex-Specific Density in Aedes albopictus: A Host Evolutionary Response to Cytoplasmic Incompatibility?

Wolbachia bacteria have invaded many arthropod species by inducing Cytoplasmic Incompatibility (CI). These symbionts represent fascinating objects of study for evolutionary biologists, but also powerful potential biocontrol agents. Here, we assess the density dynamics of Wolbachia infections in males and females of the mosquito Aedes albopitcus, an important vector of human pathogens, and interpret the results within an evolutionary framework.Wolbachia densities were measured in natural populations and in age controlled mosquitoes using quantitative PCR. We show that the density dynamics of the wAlbA Wolbachia strain infecting Aedes albopictus drastically differ between males and females, with a very rapid decay of infection in males only.Theory predicts that Wolbachia and its hosts should cooperate to improve the transmission of infection to offspring, because only infected eggs are protected from the effects of CI. However, incompatible matings effectively lower the fertility of infected males, so that selection acting on the host genome should tend to reduce the expression of CI in males, for example, by reducing infection density in males before sexual maturation. The rapid decay of one Wolbachia infection in Aedes albopictus males, but not in females, is consistent with this prediction. We suggest that the commonly observed reduction in CI intensity with male age reflects a similar evolutionary process. Our results also highlight the importance of monitoring infection density dynamics in both males and females to assess the efficiency of Wolbachia-based control strategies