ABC for Temporally Sampled Genetic Data

ABC for Temporally Sampled Genetic Dat

Christology in Dialogue with Muslims: A Critical Analysis of Christian Presentations of Christ for Muslim from the Ninth and Twentieth Centuries

Available from British Library Document Supply Centre- DSC:DXN063871 / BLDSC - British Library Document Supply CentreSIGLEGBUnited Kingdo

Dominant words rise to the top by positive frequency-dependent selection

A puzzle of language is how speakers come to use the same words for particular meanings, given that there are often many competing alternatives (e.g., "sofa," "couch," "settee"), and there is seldom a necessary connection between a word and its meaning. The well-known process of random drift-roughly corresponding in this context to "say what you hear"-can cause the frequencies of alternative words to fluctuate over time, and it is even possible for one of the words to replace all others, without any form of selection being involved. However, is drift alone an adequate explanation of a shared vocabulary? Darwin thought not. Here, we apply models of neutral drift, directional selection, and positive frequency-dependent selection to explain over 417,000 word-use choices for 418 meanings in two natural populations of speakers. We find that neutral drift does not in general explain word use. Instead, some form of selection governs word choice in over 91% of the meanings we studied. In cases where one word dominates all others for a particular meaning-such as is typical of the words in the core lexicon of a language-word choice is guided by positive frequency-dependent selection-a bias that makes speakers disproportionately likely to use the words that most others use. This bias grants an increasing advantage to the common form as it becomes more popular and provides a mechanism to explain how a shared vocabulary can spontaneously self-organize and then be maintained for centuries or even millennia, despite new words continually entering the lexicon

Detecting and quantifying natural selection at two linked loci from time series data of allele frequencies with forward-in-time simulations

Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses

Musical synaesthesia in synaesthetes and its manifestation as a wider phenomenon.

This thesis has been titled 'Musical Synaesthesia in Synaesthetes and its Manifestation as a Wider Phenomenon', in order to give an indication of the broadness of the subject area that it addresses. It looks at ways in which types of association normally associated with one of the five sensory channels sometimes make connections with, and produce stimulation of, any combination of the other four. Although the thesis touches on most known perspectives of this large topic, all of which are interconnected, it focuses on just two of these areas. Firstly, it deals with a condition which affects a small minority of the population known as ·synaesthesia'. 'Synaesthesia' is derived from the Greek combining syn meaning to combine and aesthises meaning perceived by the senses. This word was coined in the 1870s, probably by Fechner. People with synaesthesia experience involuntary sensations that do not exist in the external world but which are triggered by sensations which belong to another sensory channel. There are, for example, synaesthetes that who hear sounds as colours, taste textures, or hear odours. The first of these three examples is, by far, the most common type of synaesthesia and is especiaJIy relevant to this thesis since it deals with musical synaesthesia Musical synaesthesia usually involves strong and specific colours in connection with musical sounds. This introduces the thesis' second focal point, that of music. Coloured sensations in the absence of coloured stimuli are especially frequent as responses to music and musical material is used in this thesis to test such responses. It seems likely that Messiaen was a synaesthetic musician, and possible that Skryabin was also. In a more general way, the notion of music being coloured is not confined exclusively to synaesthetes. Numerous non-synaesthetic people maintain that certain keys, intervals, chords or sounds of certain musical instruments are coloured. Given that there are more non-synaesthetic people than there are synaesthetic people, it seems likely that the former group are predominantly responsible for the gravitation towards coloured music and towards musical paintings during the second half of the second half of the nineteenth century. Therefore, the term 'synaesthesia' might arguably be used to define this phenomenon with as much validity as it is used to define the neurological condition. It is from the above standpoint that we can gain a greater understanding of a certain prevalent spirit of the late nineteenth and early twentieth century's 'age of synaesthesia'. Although this standpoint is not convincing from a neurological point of view, it is relevant to the study of the internal worlds of several musicians, writers and painters. This is my justification for writing about synaesthesia as a wider phenomenon

CodABC:A computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate bayesian computation

The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called "CodABC," to jointly estimate recombination, substitution and synonymous and nonsynonymous rates from coding data. CodABC uses approximate Bayesian computation with and without regression adjustment and implements a variety of codon models, intracodon recombination, and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum-likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-to-use examples, and can run in parallel on multicore machines.This work was supported by the Spanish Government with the “Juan de la Cierva” fellowship JCI-2011-10452 to M.A., the European Research Council (ERC Grant Agreement No. 617457) to D.P., and Fundac¸~ao para a Ci^encia e a Tecnologia (FCT) (grant EXCL/BIA-ANM/0549/2012) to J.S.L.Peer reviewe

CodABC: a computational framework to coestimate recombination, substitution, and molecular adaptation rates by approximate Bayesian computation

The estimation of substitution and recombination rates can provide important insights into the molecular evolution of protein-coding sequences. Here, we present a new computational framework, called CodABC, to jointly estimate recombination, substitution and synonymous and non-synonymous rates from coding data. CodABC uses approximate Bayesian computation (ABC) with and without regression adjustment and implements a variety of codon models, intracodon recombination and longitudinal sampling. CodABC can provide accurate joint parameter estimates from recombining coding sequences, often outperforming maximum likelihood methods based on more approximate models. In addition, CodABC allows for the inclusion of several nuisance parameters such as those representing codon frequencies, transition matrices, heterogeneity across sites or invariable sites. CodABC is freely available from http://code.google.com/p/codabc/, includes a GUI, extensive documentation and ready-touse examples, and can run in parallel on multicore machines.Ministerio de Ciencia e Innovación | Ref. JCI-2011-10452Fundação para a Ciência e a Tecnologia | Ref. EXCL/BIA-ANM/0549/201

Strategic Management of Suppliers: an Australian Case Study

This paper describes Telstra's (Australia's dominant telecommunications company) change from ad hoc to strategic management of its numerous suppliers and the resulting benefits. The need for change, recognized by top management, required careful planning and execution. The change had many ramifications; mostly beneficial but painful for some supplanted suppliers and employees reluctant to adapt to a new culture. Benefits of the new approach were: rationalization of the number of suppliers; a more rational and fruitful approach to procurement; the professionalisation of procurement personnel; classification and consequently different treatment of suppliers; and, most importantly, changing the relationship between the company and its key suppliers from one of attempted exploitation and short term thinking to long-term, mutually profitable co-operation. The changed approach required cultural change within the procurement function but suppliers came to appreciate the company's fact-based, rational, and commercial approach. Data for this study was obtained from interviews and surveys. The study demonstrates the advantages and difficulties of changing to rational procurement practices that support corporate objectives