Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

K.L. was funded by a junior research fellowship from the National Environmental Research Council, UK (NE/I020288/1, NBAF659).Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here, we present an analysis of whole genome data from a pair of cactophilic fruit flies, Drosophila mojavensis and D. arizonae, which are reproductively isolated in the wild and differ by several large inversions on three chromosomes. We found an increase in divergence at rearranged compared to colinear chromosomes. Using the density of divergent sites in short sequence blocks we fit a series of explicit models of species divergence in which gene flow is restricted to an initial period after divergence and may differ between colinear and rearranged parts of the genome. These analyses show that D. mojavensis and D. arizonae have experienced postdivergence gene flow that ceased around 270 KY ago and was significantly reduced in chromosomes with fixed inversions. Moreover, we show that these inversions most likely originated around the time of species divergence which is compatible with theoretical models that posit a role of inversions in speciation with gene flow.Publisher PDFPeer reviewe

Group study of an 'undercover' test for visuospatial neglect: Invisible cancellation can reveal more neglect than standard cancellation

Visual neglect is a relatively common deficit after brain damage, particularly strokes. Cancellation tests provide standard clinical measures of neglect severity and deficits in daily life. A recent single-case study introduced a new variation on standard cancellation. Instead of making a visible mark on each target found, the patient made invisible marks (recorded with carbon paper underneath, for later scoring). Such invisible cancellation was found to reveal more neglect than cancellation with visible marks. Here we test the generality of this. Twenty three successive cases with suspected neglect each performed cancellation with visible or invisible marks. Neglect of contralesional targets was more pronounced with invisible marks. Indeed, about half of the patients only showed neglect in this version. For cases showing more neglect with invisible marks, stronger neglect of contralesional targets correlated with more revisits to ipsilesional targets for making additional invisible marks upon them. These results indicate that cancellation with invisible marks can reveal more neglect than standard cancellation with visible marks, while still providing a practical bedside test. Our observations may be consistent with recent proposals that demands on spatial working memory (required to keep track of previously found items only when marked invisibly) can exacerbate spatial neglect

The role of the energy equation in the fragmentation of protostellar discs during stellar encounters

In this paper, we use high-resolution smoothed particle hydrodynamics (SPH) simulations to investigate the response of a marginally stable self-gravitating protostellar disc to a close parabolic encounter with a companion discless star. Our main aim is to test whether close brown dwarfs or massive planets can form out of the fragmentation of such discs. We follow the thermal evolution of the disc by including the effects of heating due to compression and shocks and a simple prescription for cooling and find results that contrast with previous isothermal simulations. In the present case we find that fragmentation is inhibited by the interaction, due to the strong effect of tidal heating, which results in a strong stabilization of the disc. A similar behaviour was also previously observed in other simulations involving discs in binary systems. As in the case of isolated discs, it appears that the condition for fragmentation ultimately depends on the cooling rate.Comment: 9 pages, 10 figures, accepted in MNRA

Universal approximation of multi-copy states and universal quantum lossless data compression

We have proven that there exists a quantum state approximating any multi-copy state universally when we measure the error by means of the normalized relative entropy. While the qubit case was proven by Krattenthaler and Slater (IEEE Trans. IT, 46, 801-819 (2000); quant-ph/9612043), the general case has been open for more than ten years. For a deeper analysis, we have solved the mini-max problem concerning `approximation error' up to the second order. Furthermore, we have applied this result to quantum lossless data compression, and have constructed a universal quantum lossless data compression

When images work faster than words: The integration of content-based image retrieval with the Northumbria Watermark Archive

Information on the manufacture, history, provenance, identification, care and conservation of paper-based artwork/objects is disparate and not always readily available. The Northumbria Watermark Archive will incorporate such material into a database, which will be made freely available on the Internet providing an invaluable resource for conservation, research and education. The efficiency of a database is highly dependant on its search mechanism. Text based mechanisms are frequently ineffective when a range of descriptive terminologies might be used i.e. when describing images or translating from foreign languages. In such cases a Content Based Image Retrieval (CBIR) system can be more effective. Watermarks provide paper with unique visual identification characteristics and have been used to provide a point of entry to the archive that is more efficient and effective than a text based search mechanism. The research carried out has the potential to be applied to any numerically large collection of images with distinctive features of colour, shape or texture i.e. coins, architectural features, picture frame profiles, hallmarks, Japanese artists stamps etc. Although the establishment of an electronic archive incorporating a CBIR system can undoubtedly improve access to large collections of images and related data, the development is rarely trouble free. This paper discusses some of the issues that must be considered i.e. collaboration between disciplines; project management; copying and digitising objects; content based image retrieval; the Northumbria Watermark Archive; the use of standardised terminology within a database as well as copyright issues

Evolutionary breeding of healthy wheat: from plot to farm

Genetically diverse Composite Cross Populations (CCPs) may be useful in environmentally variable low-input systems as an alternative to pure line varieties. They are formed by hybridising lines with diverse evolutionary origins, bulking the F1 progeny, and allowing natural selection of the progeny in successive crop environments. CCPs derived from 10 high yielding parents (YCCPs), 12 high quality parents (QCCPs), or all 22 parents (YQCCPs), were grown at four sites (2 organic, 2 conventional) in the UK; they are currently (2006) in F5. The YCCPs out yielded the QCCPs, which had better quality characteristics. Although the CCPs performed within the range of the parents, the values obtained were often better than the mean of the parents. Some population samples are now being grown on farms and other sites in England, France, Germany and Hungary

The identification and production of varieties that increase the value of oats as a profitable component of organic production

Two experiments, one comprising husked, and the other naked, oats were established at Wakelyns Agroforestry, Suffolk in October 2004 to determine traits and varieties of oats suited to organic systems, and whether growing variety mixtures conferred any advantage. Unselected F2 breeding lines were also included for selection. Husked varieties had relatively higher yields; this may have been partly the result of poor establishment in the naked varieties. Variety height was found to be an important characteristic; tall oat varieties out-yielded the dwarfs. Two of the three variety mixtures containing the naked oat variety Expression yielded 8 and 9 % higher than the average of the component varieties. The data will be verified in the second year of replicated trials (2005/06), which will include the best performing husked and naked varieties, and a mixture of superior IGER-bred F2 breeding lines

Sustainable production of organic wheat

The aim of the project is to use an ecological approach to analyse the interactions of a range of key agronomic variables in organic wheat production (wheat genotype, spatial arrangement of seed, seed density and wheat/white clover bi-cropping) to determine an optimal approach to improved and stabilised production. The fi rst set of data revealed that seedling competition was infl uenced by seed rate and drilling arrangement. Furthermore, the variety Hereward had increased emergence and establishment to Aristos. An interaction exists between wheat variety, seed rate and drilling arrangement on the level of canopy cover at different developmental stages – these factors are important for the suppression of weeds. The input of farmers in the selection of trial variables ensures results have a direct application to the industry. The results of yield and quality at harvest will provide further insights into the interaction of agronomic variables

Control Plane Compression

We develop an algorithm capable of compressing large networks into a smaller ones with similar control plane behavior: For every stable routing solution in the large, original network, there exists a corresponding solution in the compressed network, and vice versa. Our compression algorithm preserves a wide variety of network properties including reachability, loop freedom, and path length. Consequently, operators may speed up network analysis, based on simulation, emulation, or verification, by analyzing only the compressed network. Our approach is based on a new theory of control plane equivalence. We implement these ideas in a tool called Bonsai and apply it to real and synthetic networks. Bonsai can shrink real networks by over a factor of 5 and speed up analysis by several orders of magnitude.Comment: Extended version of the paper appearing in ACM SIGCOMM 201