Probability that a chromosome is lost without trace under the neutral Wright-Fisher model with recombination

I describe an analytical approximation for calculating the short-term probability of loss of a chromosome under the neutral Wright-Fisher model with recombination. I also present an upper and lower bound for this probability. Exact analytical calculation of this quantity is difficult and computationally expensive because the number of different ways in which a chromosome can be lost, grows very large in the presence of recombination. Simulations indicate that the probabilities obtained using my approximate formula are always comparable to the true expectations provided that the number of generations remains small. These results are useful in the context of an algorithm that we recently developed for simulating Wright-Fisher populations forward in time. C++ programs that can efficiently calculate these formulas are available on request.Comment: Additional Information, Padhukasahasram et al. 2008, Genetics, FORWSIM algorith

Bacterial microevolution and the Pangenome

The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history

The makeshift city: towards a global geography of squatting

This paper introduces a set of analytical frames that explore the possibilities of conceiving, researching and writing a global geography of squatting. The paper argues that it is possible to detect, in the most tenuous of urban settings, ways of thinking about and living urban life that have the potential to reanimate the city as a key site of geographical inquiry. The paper develops a modest theory of ‘urban combats’ to account for the complexity and provisionality of squatting as an informal set of practices, as a makeshift approach to housing and as a precarious form of inhabiting the city

The autonomous city: towards a critical geography of occupation

This paper explores the recent resurgence of occupation-based practices across the globe, from the seizure of public space to the assembling of improvised protest camps. It re-examines the relationship between the figure of occupation and the affirmation of an alternative ‘right to the city’. The paper develops a critical understanding of occupation as a political process that prefigures and materializes the social order which it seeks to enact. The paper highlights the constituent role of occupation as an autonomous form of urban dwelling, as a radical politics of infrastructure and as a set of relations that produce common spaces for political action

The Population Genetics of dN/dS

Evolutionary pressures on proteins are often quantified by the ratio of substitution rates at non-synonymous and synonymous sites. The dN/dS ratio was originally developed for application to distantly diverged sequences, the differences among which represent substitutions that have fixed along independent lineages. Nevertheless, the dN/dS measure is often applied to sequences sampled from a single population, the differences among which represent segregating polymorphisms. Here, we study the expected dN/dS ratio for samples drawn from a single population under selection, and we find that in this context, dN/dS is relatively insensitive to the selection coefficient. Moreover, the hallmark signature of positive selection over divergent lineages, dN/dS>1, is violated within a population. For population samples, the relationship between selection and dN/dS does not follow a monotonic function, and so it may be impossible to infer selection pressures from dN/dS. These results have significant implications for the interpretation of dN/dS measurements among population-genetic samples

Unexpected high diversity of galling insects in the Amazonian upper canopy: The savanna out there

A relatively large number of studies reassert the strong relationship between galling insect diversity and extreme hydric and thermal status in some habitats, and an overall pattern of a greater number of galling species in the understory of scleromorphic vegetation. We compared galling insect diversity in the forest canopy and its relationship with tree richness among upland terra firme, várzea, and igapó floodplains in Amazonia, Brazil. The soils of these forest types have highly different hydric and nutritional status. Overall, we examined the upper layer of 1,091 tree crowns. Galling species richness and abundance were higher in terra firme forests compared to várzea and igapó forests. GLM-ANCOVA models revealed that the number of tree species sampled in each forest type was determinant in the gall-forming insect diversity. The ratio between galling insect richness and number of tree species sampled (GIR/TSS ratio) was higher in the terra firme forest and in seasonally flooded igapó, while the várzea presented the lowest GIR/TSS ratio. In this study, we recorded unprecedented values of galling species diversity and abundance per sampling point. The GIR/TSS ratio from várzea was approximately 2.5 times higher than the highest value of this ratio ever reported in the literature. Based on this fact, we ascertained that várzea and igapó floodplain forests (with lower GIA and GIR), together with the speciose terra firme galling community emerge as the gall diversity apex landscape among all biogeographic regions already investigated. Contrary to expectation, our results also support the "harsh environment hypothesis", and unveil the Amazonian upper canopy as similar to vegetation habitats, hygrothermically stressed environments with temperature at lethal limits and high levels of leaf sclerophylly. © 2014 Julião et al

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It is a standard practice to test for the signature of homologous recombination in studies examining the genetic diversity of bacterial populations. Although it has emerged that homologous recombination rates can vary widely between species, comparing the results from different studies is made difficult by the diversity of estimation methods used. Here, Multi Locus Sequence Typing (MLST) datasets from a wide variety of bacteria and archaea are analyzed using the ClonalFrame method. This enables a direct comparison between species and allows for a first exploration of the question whether phylogeny or ecology is the primary determinant of homologous recombination rate

Population genetics from 1966 to 2016

We describe the astonishing changes and progress that have occurred in the field of population genetics over the past 50 years, slightly longer than the time since the first Population Genetics Group (PGG) meeting in January 1968. We review the major questions and controversies that have preoccupied population geneticists during this time (and were often hotly debated at PGG meetings). We show how theoretical and empirical work has combined to generate a highly productive interaction involving successive developments in the ability to characterise variability at the molecular level, to apply mathematical models to the interpretation of the data and to use the results to answer biologically important questions, even in nonmodel organisms. We also describe the changes from a field that was largely dominated by UK and North American biologists to a much more international one (with the PGG meetings having made important contributions to the increased number of population geneticists in several European countries). Although we concentrate on the earlier history of the field, because developments in recent years are more familiar to most contemporary researchers, we end with a brief outline of topics in which new understanding is still actively developing

Structure and dynamics of methyl groups in the deuterated microporous organic-inorganic hybrid, aluminium methylphosphonate-b

Neutron powder diffraction at 4.6 K and H-2 NMR spectroscopy over the range 100-400 K have been used to examine the structure and rotational dynamics of CD3 groups pointing into the unidimensional channels of the beta-polymorph of the hybrid organic/inorganic microporous solid aluminium methylphosphonate, Al-2(CD3PO3)(3), The methyl groups rotate rapidly at all temperatures studied in the NMR experiments, with a correlation time in the fast limit of similar to 2 x 10(-13) s and with an activation energy of similar to 10 kT mol(-1). Extrapolation to 4.6 K indicates that the groups will be stationary and this is confirmed by the neutron diffraction experiment, where the lowest-energy configurations of the methylphosphonate groups are all found to have the methyl deuterons staggered with respect to the phosphonate oxygens. (C) 1999 Elsevier Science B.V. All rights reserved.</p