Inferring the intensity of positive selection in protein-coding genes is important since it is used to shed light on the process of adaptation. Recently, it has been reported that overlapping genes, which are ubiquitous in all domains of life, seem to exhibit inordinate degrees of positive selection. Here, we present a new method for the simultaneous estimation of selection intensities in overl...

We investigate the evolution of a multigene family incorporating the forces of drift, mutation, gene conversion, unequal crossing over and selection. The use of simulation studies is required due to the complexity of the model. Selection is modeled in two modes: positive selection as a function of the number of different beneficial alleles and negative selection against deleterious alleles. We ...

Changes in gene expression may represent an important mode of human adaptation. However, to date, there are relatively few known examples in which selection has been shown to act directly on levels or patterns of gene expression. In order to test whether single nucleotide polymorphisms (SNPs) that affect gene expression in cis are frequently targets of positive natural selection in humans, we a...

Past demographic changes can produce distortions in patterns of genetic variation that can mimic the appearance of natural selection unless the demographic effects are explicitly removed. Here we fit a detailed model of human demography that incorporates divergence, migration, admixture, and changes in population size to directly sequenced data from 13,400 protein coding genes from 20 European-...

There has recently been considerable interest in detecting natural selection in the human genome. Selection will usually tend to increase identity-by-descent (IBD) among individuals in a population, and many methods for detecting recent and ongoing positive selection indirectly take advantage of this. In this article we show that excess IBD sharing is a general property of natural selection and...

VlJl rearrangements obtained from genomic DNA of individual IgM B cells from human fetal spleen were analyzed. A nonrandom pattern of l gene rearrangements that differed from the adult Vl repertoire was found. The Vl distal genes 8A and 4B were absent from the nonproductive fetal repertoire, whereas 2E and 3L were overrepresented and 1B was underrepresented in the productive fetal repertoire. P...

The feature selection characterized by relatively small sample size and extremely high dimensional feature space is common in many areas of contemporary statistics. The high dimensionality of the feature space causes serious difficulties: (i) the sample correlations between features become high even if the features are stochastically independent; (ii) the computation becomes intractable. These ...

In the age of next-generation sequencing, the availability of increasing amounts and improved quality of data at decreasing cost ought to allow for a better understanding of how natural selection is shaping the genome than ever before. However, alternative forces, such as demography and background selection (BGS), obscure the footprints of positive selection that we would like to identify. In t...

Negative selection algorithms generate their detector sets based on the points of self data. In the approach described in this paper, the continuous self region is defined by the collection of self data. This has important differences from the negative selection algorithms that simply take each self point and its vicinity as the self region: when the training self points are used together as a ...

Distinguishing the relative roles of positive and negative selection along with demographic history in shaping genetic diversity has been a decades-long endeavor. Understanding the forces structuring genetic variation informs us not only about the factors maintaining diversity but also about the fundamental evolutionary parameters that influence natural populations, including the rate and stren...