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Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein–Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. [ABSTRACT FROM AUTHOR]

Abstract: Using the fossil record yields more detailed reconstructions of the evolutionary process than what is obtained from contemporary lineages only. In this work, we present a stochastic process modeling not only speciation and extinction, but also fossil finds. Next, we derive an explicit formula for the likelihood of a reconstructed phylogeny with fossils, which can be used to estimate the speciation and extinction rates. Finally, we provide a comparative simulation-based evaluation of the accuracy of estimations of these rates from complete phylogenies (including extinct lineages), from reconstructions with contemporary lineages only and from reconstructions with contemporary lineages and the fossil record. Results show that taking the fossil record into account yields more accurate estimates of speciation and extinction rates than considering only contemporary lineages. [Copyright &y& Elsevier]

Markets with asymmetrical information are generally studied from a wealth optimization point of view. We focus here on a hedging problem for a financial agent who has an additional information on the market. We extend the results given for hedging strategies with fixed terminal time to the case of a random terminal time. In particular, we provide tools to understand the behavior of American option hedging by an insider. To achieve this aim, we prove the existence and uniqueness of backward stochastic differential equations solutions, when terminal time is random, under an initially enlarged filtration. [ABSTRACT FROM AUTHOR]

Studies of animal movements have been popularized for many large and shy species by the increasing use of radio telemetry methods (VHF and GPS technologies). Data are collected with high sampling frequency, and consist of successive observations of the position of an individual animal. The statistical analysis of such data poses several problems due to the lack of independence of successive observations. However, the statistical description of the temporal autocorrelation between successive steps is rarely performed by ecologists studying the patterns of animals movements. The aim of this paper is to warn ecologists against the consequences of failing to consider this aspect. We discuss the various issues related to analyzing autocorrelated data, and show how the exploratory analysis of autocorrelation can both reveal important biological insights and help to improve the accuracy of movement models. We suggest some tools that can be used to measure, test, and adjust for temporal autocorrelation. A short ecological illustration is presented. [ABSTRACT FROM AUTHOR]

Background: Genome size and gene content in bacteria are associated with their lifestyles. Obligate intracellular bacteria (i.e., mutualists and parasites) have small genomes that derived from larger free-living bacterial ancestors; however, the different steps of bacterial specialization from free-living to intracellular lifestyle have not been studied comprehensively. The growing number of available sequenced genomes makes it possible to perform a statistical comparative analysis of 317 genomes from bacteria with different lifestyles. Results: Compared to free-living bacteria, host-dependent bacteria exhibit fewer rRNA genes, more split rRNA operons and fewer transcriptional regulators, linked to slower growth rates. We found a function-dependent and non-random loss of the same 100 orthologous genes in all obligate intracellular bacteria. Thus, we showed that obligate intracellular bacteria from different phyla are converging according to their lifestyle. Their specialization is an irreversible phenomenon characterized by translation modification and massive gene loss, including the loss of transcriptional regulators. Although both mutualists and parasites converge by genome reduction, these obligate intracellular bacteria have lost distinct sets of genes in the context of their specific host associations: mutualists have significantly more genes that enable nutrient provisioning whereas parasites have genes that encode Types II, IV, and VI secretion pathways. Conclusion: Our findings suggest that gene loss, rather than acquisition of virulence factors, has been a driving force in the adaptation of parasites to eukaryotic cells. This comparative genomic analysis helps to explore the strategies by which obligate intracellular genomes specialize to particular host-associations and contributes to advance our knowledge about the mechanisms of bacterial evolution. [ABSTRACT FROM AUTHOR]

Abstract: We studied the possible effects of the expansion of ancient Mediterranean civilizations during the five centuries before and after Christ on the European distribution of the mutant allele for the chemokine receptor gene CCR5 which has a 32-bp deletion (CCR5-Δ32). There is a strong evidence for the unitary origin of the CCR5-Δ32 mutation, this it is found principally in Europe and Western Asia, with generally a north–south downhill cline frequency. Homozygous carriers of this mutation show a resistance to HIV-1 infection and a slower progression towards AIDS. However, HIV has clearly emerged too recently to have been the selective force on CCR5. Our analyses showed strong negative correlations in Europe between the allele frequency and two historical parameters, i.e. the first colonization dates by the great ancient Mediterranean civilizations, and the distances from the Northern frontiers of the Roman Empire in its greatest expansion. Moreover, other studies have shown that the deletion frequencies in both German Bronze Age and Swedish Neolithic populations were similar to those found in the corresponding modern populations, and this deletion has been found in ancient DNA of around 7000 years ago, suggesting that in the past, the deletion frequency could have been relatively high in European populations. In addition, in West Nile virus pathogenesis, CCR5 plays an antimicrobial role showing that host genetic factors are highly pathogen-specific. Our results added to all these previous data suggest that the actual European allele frequency distribution might not be due to genes spreading, but to a negative selection resulting in the spread of pathogens principally during Roman expansion. Indeed, as gene flows from colonizers to European native populations were extremely low, the mutational changes might be associated with vulnerability to imported infections. To date, the nature of the parasites remains unknown; however, zoonoses could be incriminated. [Copyright &y& Elsevier]

• We determine the distribution of independent contrast for traits under linear trend. • Show that the standard independent contrasts coont be used to test for correlation in this case. • Provide a method to correct linear trends. • Which performs better than three previous approaches on data simulated under directional evolution. Being confounding factors, directional trends are likely to make two quantitative traits appear as spuriously correlated. By determining the probability distributions of independent contrasts when traits evolve following Brownian motions with linear trends, we show that the standard independent contrasts can not be used to test for correlation in this situation. We propose a multiple regression approach which corrects the bias caused by directional evolution. We show that our approach is equivalent to performing a Phylogenetic Generalized Least Squares (PGLS) analysis with tip times as covariables by providing a new and more general proof of the equivalence between PGLS and independent contrasts methods. Our approach is assessed and compared with three previous correlation tests on data simulated in various situations and overall outperforms all the other methods. The approach is next illustrated on a real dataset to test for correlation between hominin cranial capacity and body mass. [ABSTRACT FROM AUTHOR]

It is well known that horizontal gene transfer (HGT) is a major force in the evolution of prokaryotes. During the adaptation of a bacterial population to a new ecological niche, and particularly for intracellular bacteria, selective pressures are shifted and ecological niches reduced, resulting in a lower rate of genetic connectivity. HGT and positive selection are therefore two important evolutionary forces in microbial pathogens that drive adaptation to new hosts. In this study, we use genomic distance analyses, phylogenomic networks, tree topology comparisons, and Bayesian inference methods to investigate to what extent HGT has occurred during the evolution of the genus Rickettsia, the effect of the use of different genomic regions in estimating reticulate evolution and HGT events, and the link of these to host range. We show that ecological specialization restricts recombination occurrence in Rickettsia, but other evolutionary processes and genome architecture are also important for the occurrence of HGT. We found that recombination, genomic rearrangements, and genome conservation all show evidence of network-like evolution at whole-genome scale. We show that reticulation occurred mainly, but not only, during the early Rickettsia radiation, and that core proteome genes of every major functional category have experienced reticulated evolution and possibly HGT. Overall, the evolution of Rickettsia bacteria has been tree-like, with evidence of HGT and reticulated evolution for around 10–25% of the core Rickettsia genome. We present evidence of extensive recombination/incomplete lineage sorting (ILS) during the radiation of the genus, probably linked with the emergence of intracellularity in a wide range of hosts. [ABSTRACT FROM AUTHOR]

Background The two main puzzles of this study are the onset and then sudden stopping of severe epidemics in western Provence (a highly malaria-endemic region of Mediterranean France) without any deliberate counter-measures and in the absence of significant population flux. Methods Malaria epidemics during the period from 1745 to 1850 were analysed against temperature and rainfall records and several other potentially relevant factors. Results Statistical analyses indicated that relatively high temperatures in early spring and in September/October, rainfall during the previous winter (principally December) and even from November to September and epidemics during the previous year could have played a decisive role in the emergence of these epidemics. Moreover, the epidemics were most likely not driven by other parameters (e.g., social, cultural, agricultural and geographical). Until 1776, very severe malarial epidemics affected large areas, whereas after this date, they were rarer and generally milder for local people and were due to canal digging activities. In the latter period, decreased rainfall in December, and more extreme and variable temperatures were observed. It is known that rainfall anomalies and temperature fluctuations may be detrimental to vector and parasite development. Conclusion This study showed the particular characteristics of malaria in historical Provence. Contrary to the situation in most other Mediterranean areas, Plasmodium falciparum was most likely not involved (during the years with epidemics, the mean temperature during the months of July and August, among other factors, did not play a role) and the population had no protective mutation. The main parasite species was Plasmodium vivax, which was responsible for very severe diseases, but contrary to in northern Europe, it is likely that transmission occurred only during the period where outdoor sporogony was possible, and P. vivax sporogony was always feasible, even during colder summers. Possible key elements in the understanding of the course of malaria epidemics include changes in the virulence of P. vivax strains, the refractoriness of anophelines and/or the degree or efficiency of acquired immunity. This study could open new lines of investigation into the comprehension of the conditions of disappearance/emergence of severe malaria epidemics in highly endemic areas. [ABSTRACT FROM AUTHOR]