5,216 research outputs found
Inferring the Distribution of Selective Effects from a Time Inhomogeneous Model
We have developed a Poisson random field model for estimating the distribution of selective effects of newly arisen nonsynonymous mutations that could be observed as polymorphism or divergence in samples of two related species under the assumption that the two species populations are not at mutation-selection-drift equilibrium. The model is applied to 91Drosophila genes by comparing levels of polymorphism in an African population of D. melanogaster with divergence to a reference strain of D. simulans. Based on the difference of gene expression level between testes and ovaries, the 91 genes were classified as 33 male-biased, 28 female-biased, and 30 sex-unbiased genes. Under a Bayesian framework, Markov chain Monte Carlo simulations are implemented to the model in which the distribution of selective effects is assumed to be Gaussian with a mean that may differ from one gene to the other to sample key parameters. Based on our estimates, the majority of newly-arisen nonsynonymous mutations that could contribute to polymorphism or divergence in Drosophila species are mildly deleterious with a mean scaled selection coefficient of -2.81, while almost 86% of the fixed differences between species are driven by positive selection. There are only 16.6% of the nonsynonymous mutations observed in sex-unbiased genes that are under positive selection in comparison to 30% of male-biased and 46% of female-biased genes that are beneficial. We also estimated that D. melanogaster and D. simulans may have diverged 1.72 million years ago
Linguistic Reflection in Java
Reflective systems allow their own structures to be altered from within. Here
we are concerned with a style of reflection, called linguistic reflection,
which is the ability of a running program to generate new program fragments and
to integrate these into its own execution. In particular we describe how this
kind of reflection may be provided in the compiler-based, strongly typed
object-oriented programming language Java. The advantages of the programming
technique include attaining high levels of genericity and accommodating system
evolution. These advantages are illustrated by an example taken from persistent
programming which shows how linguistic reflection allows functionality (program
code) to be generated on demand (Just-In-Time) from a generic specification and
integrated into the evolving running program. The technique is evaluated
against alternative implementation approaches with respect to efficiency,
safety and ease of use.Comment: 25 pages. Source code for examples at
http://www-ppg.dcs.st-and.ac.uk/Java/ReflectionExample/ Dynamic compilation
package at http://www-ppg.dcs.st-and.ac.uk/Java/DynamicCompilation
Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal
Acknowledgements This work was funded by BBSRC research project BB/J00336/1. FS and a part of the proportion of the cost of the Illumina genotyping was funded by a Beachell-Borlag International Fellowship. The authors would like to acknowledge the help of Dr MK Sarmah in collecting seed samples of the landraces and improved cultivars from Assam used in this study and Dr. Ma. Elizabeth B. Naredo and Ms. Sheila Mae Q. Mercado for handling of IRGC accessions and preparation of DNAs for genotyping. All rice seeds used here were obtained with MTA agreements and seed and dry leaves imported into the UK under import licence IMPâSOILâ18â2009 issued by Science and Advice for Scottish Agriculture.Peer reviewedPublisher PD
PHYLOGENETIC RELATIONSHIPS AMONG WEST INDIAN XENODONTINE SNAKES (SERPENTES; COLUBRIDAE) WITH COMMENTS ON THE PHYLOGENY OF SOME MAINLAND XENODONTINES
The evolutionary relationships of the West Indian (W. I.) xenodontine snake assemblage has been considered as either monophyletic or paraphyletic. Allozyme data from protein electrophoresis were used to estimate the phylogeny of the W. I. xenodontine snakes. Forty-two species from 25 genera (mainland and W. I. taxa) were examined. The phylogenetic relationships were estimated using parsimony analyses with successive approximation weighting on the data coded two ways: (1) the allele as the character and (2) the locus as the character. The most parsimonious trees from both coding methods indicated a non-monophyletic W. I. xenodontine assemblage. Three W.I. groups were recovered in both coding methods: (1) Jamaican Arrhyton and Darlingtonia, (2) Uromacer and the Cuban Arrhyton, and (3) Alsophis, Ialtris, and the South American Alsophis elegans. The relationships of Hypsirhynchus, Antillophis and Arrhyton exiguum were unstable. Nomenclatural changes are recommended for Darlingtonia, Arrhyton, Ialtris and Alsophis
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