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 ...

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-...

This paper investigates the role of negative selection in an artificial immune system (AIS) for network intrusion detection. The work focuses on the use of negative selection as a network traffic anomaly detector. The results of the negative selection algorithm experiments show a severe scaling problem for handling real network traffic data. The paper concludes by suggesting that the most appro...

On the basis of the polyclonal selection algorithm, an improved polyclonal selection algorithm based on negative selection is put forward in this paper. Inspired by the diversity and auto-tolerance of the negative selection, the population diversity is increased by the clone deletion and clone supply to improve the polyclonal selection algorithm. Finally, the optimization design of the crane bo...

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...

We present a novel composite-likelihood-ratio test (CLRT) for detecting genes and genomic regions that are subject to recurrent natural selection (either positive or negative). The method uses the likelihood functions of Hartl et al. (1994) for inference in a Wright-Fisher genic selection model and corrects for nonindependence among sites by application of coalescent simulations with recombinat...