The animal chemosensory system is involved in essential biological processes, most of them mediated by proteins encoded in multigene families. These multigene families have been fundamental for the adaptation to new environments, significantly contributing to phenotypic variation. This adaptive potential contrasts, however, with the lack of studies at their upstream regions, especially taking i...

How CD4(+)CD8(+) thymocytes commit to CD4 helper versus CD8 cytotoxic lineages is a central unresolved question in developmental immunology. In this issue, show that engineering CD4 for shutoff immediately after positive selection misdirects cells to the cytotoxic lineage. The result highlights the distinction between positive selection and lineage commitment and provides new impetus for reexam...

Rapid and inexpensive sequencing technologies are making it possible to collect whole genome sequence data on multiple individuals from a population. This type of data can be used to quickly identify genes that control important ecological and evolutionary phenotypes by finding the targets of adaptive natural selection, and we therefore refer to such approaches as "reverse ecology." To quantify...

Coalescent theory is a powerful tool for population geneticists as well as molecular biologists interested in understanding the patterns and levels of DNA variation. Using coalescent Monte Carlo simulations it is possible to obtain the empirical distributions for a number of statistics across a wide range of evolutionary models; these distributions can be used to test evolutionary hypotheses us...

The distribution of genetic polymorphisms in a population contains information about evolutionary processes. The Poisson random field (PRF) model uses the polymorphism frequency spectrum to infer the mutation rate and the strength of directional selection. The PRF model relies on an infinite-sites approximation that is reasonable for most eukaryotic populations, but that becomes problematic whe...

Recent studies have reported evidence suggesting that portions of contemporary human genomes introgressed from archaic hominin populations went to high frequencies due to positive selection. However, no study to date has specifically addressed the post-introgression population dynamics of these putative cases of adaptive introgression. Here, for the first time, we specifically define cases of i...

Attempts to determine or to select what kind of person or people to bring into existence are controversial. This is particularly true of “negative selection” or “selecting against” a certain type of person—that is, the attempt to prevent a person of a certain type, or people of that type, from existing. Virtually everyone agrees that some instances of negative selection are objectionable—for ex...

Creation of defined genetic mutations is a powerful method for dissecting mechanisms of bacterial disease; however, many genetic tools are only developed for laboratory strains. We have designed a modular and general negative selection strategy based on inducible toxins that provides high selection stringency in clinical Escherichia coli and Salmonella isolates. No strain- or species-specific o...

We present a maximum-likelihood method for examining the selection pressure and detecting positive selection in noncoding regions using multiple aligned DNA sequences. The rate of substitution in noncoding regions relative to the rate of synonymous substitution in coding regions is modeled by a parameter zeta. When a site in a noncoding region is evolving neutrally zeta = 1, while zeta > 1 indi...

The T cell alphabeta receptor (TCR) recognizes foreign peptide antigens bound to proteins encoded in the MHC. The MHC portion of this complex contributes much to the footprint of the TCR on the ligand, yet T cells are usually very specific for individual foreign peptides. Here, we show that the development of peptide-specific T cells is not intrinsic to thymocytes that undergo thymic-positive s...