Measurement error and rank correlations

This paper characterizes and proposes a method to correct for errors-in-variables biases in the estimation of rank correlation coefficients (Spearman’s ρ and Kendall’s τ ). We first investigate a set of sufficient conditions under which measurement errors bias the sample rank correlations toward zero. We then provide a feasible nonparametric bias-corrected estimator based on the technique of small error variance approximation. We assess its performance in simulations and an empirical application, using rich Swedish data to estimate intergenerational rank correlations in income. The method performs well in both cases, lowering the mean squared error by 50-85 percent already in moderately sized samples (n = 1, 000)

Content Scheduling in Multimedia Interactive Mobile Games

In this paper, we study how to implement interactive multimedia services using a DVB-H broadcast channel combined with a point-to-point channel, such as 3G or GPRS. We study the problem in the context of a location-based interactive mobile game. The technical challenge is to schedule the sending of data over the broadcast channel while maintaining Quality-of-Service, that is, sending the right data to the right user at the right time to provide a seamless interactive experience. We explore design issues and problems related to the scheduling of content in the game, present a usecase study to describe scheduling problems and propose a content scheduling algorithm to solve these problems. Moreover, we provide a simulation of the system and the experimental results to show how different game parameters influence the in-time delivery of the multimedia content to the players. We conclude that most of the problems involved with our approach can be expressed as the problem of defining delivery deadlines for a scheduling algorithm

Untangling the hedge: Genetic diversity in clonally and sexually transmitted genomes of European wild roses, Rosa L.

While European wild roses are abundant and widely distributed, their morphological taxonomy is complicated and ambiguous. In particular, the polyploid Rosa section Caninae (dogroses) is characterised by its unusual meiosis, causing simultaneous clonal and sexual transmission of sub-genomes. This hemisexual reproduction, which often co-occurs with vegetative reproduction, defies the standard definition of species boundaries. We analysed seven highly polymorphic microsatellite loci, scored for over 2 600 Rosa samples of differing ploidy, collected across Europe within three independent research projects. Based on their morphology, these samples had been identified as belonging to 21 dogrose and five other native rose species. We quantified the degree of clonality within species and at individual sampling sites. We then compared the genetic structure within our data to current rose morpho-systematics and searched for hemisexually co-inherited sets of alleles at individual loci. We found considerably fewer copies of identical multi-locus genotypes in dogroses than in roses with regular meiosis, with some variation recorded among species. While clonality showed no detectable geographic pattern, some genotypes appeared to be more widespread. Microsatellite data confirmed the current classification of subsections, but they did not support most of the generally accepted dogrose microspecies. Under canina meiosis, we found co-inherited sets of alleles as expected, but could not distinguish between sexually and clonally inherited sub-genomes, with only some of the detected allele combinations being lineage-specific

Combining genetic resources and elite material populations to improve the accuracy of genomic prediction in apple

Genomic selection is an attractive strategy for apple breeding that could reduce the length of breeding cycles. A possible limitation to the practical implementation of this approach lies in the creation of a training set large and diverse enough to ensure accurate predictions. In this study, we investigated the potential of combining two available populations, i.e., genetic resources and elite material, in order to obtain a large training set with a high genetic diversity. We compared the predictive ability of genomic predictions within-population, across-population or when combining both populations, and tested a model accounting for population-specific marker effects in this last case. The obtained predictive abilities were moderate to high according to the studied trait and small increases in predictive ability could be obtained for some traits when the two populations were combined into a unique training set. We also investigated the potential of such a training set to predict hybrids resulting from crosses between the two populations, with a focus on the method to design the training set and the best proportion of each population to optimize predictions. The measured predictive abilities were very similar for all the proportions, except for the extreme cases where only one of the two populations was used in the training set, in which case predictive abilities could be lower than when using both populations. Using an optimization algorithm to choose the genotypes in the training set also led to higher predictive abilities than when the genotypes were chosen at random. Our results provide guidelines to initiate breeding programs that use genomic selection when the implementation of the training set is a limitation

Genotype calling in tetraploid species from bi-allelic marker data using mixture models

<p>Abstract</p> <p>Background</p> <p>Automated genotype calling in tetraploid species was until recently not possible, which hampered genetic analysis. Modern genotyping assays often produce two signals, one for each allele of a bi-allelic marker. While ample software is available to obtain genotypes (homozygous for either allele, or heterozygous) for diploid species from these signals, such software is not available for tetraploid species which may be scored as five alternative genotypes (aaaa, baaa, bbaa, bbba and bbbb; nulliplex to quadruplex).</p> <p>Results</p> <p>We present a novel algorithm, implemented in the R package fitTetra, to assign genotypes for bi-allelic markers to tetraploid samples from genotyping assays that produce intensity signals for both alleles. The algorithm is based on the fitting of several mixture models with five components, one for each of the five possible genotypes. The models have different numbers of parameters specifying the relation between the five component means, and some of them impose a constraint on the mixing proportions to conform to Hardy-Weinberg equilibrium (HWE) ratios. The software rejects markers that do not allow a reliable genotyping for the majority of the samples, and it assigns a missing score to samples that cannot be scored into one of the five possible genotypes with sufficient confidence.</p> <p>Conclusions</p> <p>We have validated the software with data of a collection of 224 potato varieties assayed with an Illumina GoldenGate™ 384 SNP array and shown that all SNPs with informative ratio distributions are fitted. Almost all fitted models appear to be correct based on visual inspection and comparison with diploid samples. When the collection of potato varieties is analyzed as if it were a population, almost all markers seem to be in Hardy-Weinberg equilibrium. The R package fitTetra is freely available under the GNU Public License from <url>http://www.plantbreeding.wur.nl/UK/software_fitTetra.html</url> and as Additional files with this article.</p

Assessing Molecular Signature for Some Potential Date (Phoenix dactylifera L.) Cultivars from Saudi Arabia, Based on Chloroplast DNA Sequences rpoB and psbA-trnH

Phoenix dactylifera L. (date palm), being economically very important, is widely cultivated in the Middle East and North Africa, having about 400 different cultivars. Assessment of date cultivars under trading and farming is a widely accepted problem owing to lack of a unique molecular signature for specific date cultivars. In the present study, eight different cultivars of dates viz., Khodry, Khalas, Ruthana, Sukkari, Sefri, Segae, Ajwa and Hilali were sequenced for rpoB and psbA-trnH genes and analyzed using bioinformatics tools to establish a cultivar-specific molecular signature. The combined aligned data matrix was of 1147 characters, of which invariable and variable sites were found to be 958 and 173, respectively. The analysis clearly reveals three major groups of these cultivars: (i) Khodary, Sefri, Ajwa, Ruthana and Hilali (58% BS); (ii) Sukkari and Khalas (64% BS); and (iii) Segae. The economically most important cultivar Ajwa showed similarity with Khodary and Sefri (67% BS).The sequences of the date cultivars generated in the present study showed bootstrap values between 38% and 70% so these sequences could be carefully used as molecular signature for potential date cultivars under trading and selection of genuine cultivars at the seedling stage for farming

Academic freedom in Europe: time for a Magna Charta?

This paper is a preliminary attempt to establish a working definition of academic freedom for the European Union states. The paper details why such a definition is required for the European Union and then examines some of the difficulties of defining academic freedom. By drawing upon experience of the legal difficulties beset by the concept in the USA and building on previous analyses of constitutional and legislative protection for academic freedom, and of legal regulations concerning institutional governance and academic tenure, a working definition of academic freedom is then derived. The resultant definition which, it is suggested, could form the basis for a European Magna Charta Libertatis Academicae, goes beyond traditional discussions of academic freedom by specifying not only the rights inherent in the concept but also its accompanying duties, necessary limitations and safeguards. The paper concludes with proposals for how the definition might be tested and carried forward

Reconstruction of multi-generation pedigrees involving numerous old apple cultivars thanks to whole-genome SNP data

A number of European apple cultivars are old, some of them dating back to the Renaissance, Middle Ages or even earlier. Many other cultivars have been developed during subsequent times. In order to decipher the relationships that link some of these old cultivars, whole-genome SNP data (~ 250K) for over 1400 genotypes were analyzed to infer first-degree relationships and reconstruct pedigrees. We used simple exclusion tests based on a count of Mendelian error to identify up to a thousand potential parent-offspring duos, including 295 complete parent-offspring trios and a hundred duos that could be oriented. grand-parents for some missing parents could also be inferred. Combining all this information allowed us to reconstruct pedigrees (up to 6 generations) highlighting the central role of major founders such as ‘Reinette Franche’, ‘Margil’, and ‘Alexander’. Haplotypes were deduced from genotypic data and pedigrees, and used to measure haplotype sharing between supposedly unrelated cultivars, allowing investigating further links between them.To our knowledge, such a large analysis to reconstruct multigeneration pedigrees involving (very) old cultivars selected over such time has never before been performed in perennial fruit species

Influence of phenological barriers and habitat differentiation on the population genetic structure of the balearic endemic Rhamnus ludovici-salvatoris Chodat and R. alaternus L

[EN] Rhamnus ludovici-salvatoris, endemic to the Gymnesian Islands, coexists with the related and widespread R. alaternus in Mallorca and Menorca. In both species, the population genetic structure using RAPD, and flowering during a 3-year period to check for possible phenological barriers, were analyzed. Rhamnus ludovici-salvatoris showed lower genetic diversity and stronger population structure than R. alaternus, the Cabrera population being less diverse and the most differentiated. Rhamnus ludovici-salvatoris flowered one month later, although flowering of both species coincided sporadically. These congeners seem to have diverged through isolation by time and differentiation in habitat. The population genetic structure of R. ludovici-salvatoris could mainly be due to the existence of small populations on the one hand, and a gene flow caused by rare hybridization events on the other, which may also explain the presence of morphologically intermediate individuals in Menorca. 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