Nonadaptive explanations for signatures of partial selective sweeps in Drosophila.

A beneficial mutation that has nearly but not yet fixed in a population produces a characteristic haplotype configuration, called a partial selective sweep. Whether nonadaptive processes might generate similar haplotype configurations has not been extensively explored. Here, we consider 5 population genetic data sets taken from regions flanking high-frequency transposable elements in North American strains of Drosophila melanogaster, each of which appears to be consistent with the expectations of a partial selective sweep.

The application of statistical physics to evolutionary biology.

A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and the load in finite populations.

Functional genomic analysis of the rates of protein evolution.

The evolutionary rates of proteins vary over several orders of magnitude. Recent work suggests that analysis of large data sets of evolutionary rates in conjunction with the results from high-throughput functional genomic experiments can identify the factors that cause proteins to evolve at such dramatically different rates. To this end, we estimated the evolutionary rates of >3,000 proteins in four species of the yeast genus Saccharomyces and investigated their relationship with levels of expression and protein dispensability.

Adjusting for selection on synonymous sites in estimates of evolutionary distance.

Evolution at silent sites is often used to estimate the pace of selectively neutral processes or to infer differences in divergence times of genes. However, silent sites are subject to selection in favor of preferred codons, and the strength of such selection varies dramatically across genes. Here, we use the relationship between codon bias and synonymous divergence observed in four species of the genus Saccharomyces to provide a simple correction for selection on silent sites.

Coevolution of gene expression among interacting proteins.

Physically interacting proteins or parts of proteins are expected to evolve in a coordinated manner that preserves proper interactions. Such coevolution at the amino acid-sequence level is well documented and has been used to predict interacting proteins, domains, and amino acids. Interacting proteins are also often precisely coexpressed with one another, presumably to maintain proper stoichiometry among interacting components.

Evolutionary rate depends on number of protein-protein interactions independently of gene expression level.

Background: Whether or not a protein's number of physical interactions with other proteins plays a role in determining its rate of evolution has been a contentious issue. A recent analysis suggested that the observed correlation between number of interactions and evolutionary rate may be due to experimental biases in high-throughput protein interaction data sets.

Discussion: The number of interactions per protein, as measured by some protein interaction data sets, shows no correlation with evolutionary rate.

Noise minimization in eukaryotic gene expression.

All organisms have elaborate mechanisms to control rates of protein production. However, protein production is also subject to stochastic fluctuations, or "noise." Several recent studies in Saccharomyces cerevisiae and Escherichia coli have investigated the relationship between transcription and translation rates and stochastic fluctuations in protein levels, or more generally, how such randomness is a function of intrinsic and extrinsic factors.

Stable association between strains of Mycobacterium tuberculosis and their human host populations.

Mycobacterium tuberculosis is an important human pathogen in virtually every part of the world. Here we investigate whether distinct strains of M. tuberculosis infect different human populations and whether associations between host and pathogen populations are stable despite global traffic and the convergence of diverse strains of the pathogen in cosmopolitan urban centers.

Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains.

To better understand genome function and evolution in Mycobacterium tuberculosis, the genomes of 100 epidemiologically well characterized clinical isolates were interrogated by DNA microarrays and sequencing. We identified 68 different large-sequence polymorphisms (comprising 186,137 bp, or 4.2% of the genome) that are present in H37Rv, but absent from one or more clinical isolates.

On the use of star-shaped genealogies in inference of coalescence times.

Genealogies from rapidly growing populations have approximate "star" shapes. We study the degree to which this approximation holds in the context of estimating the time to the most recent common ancestor (T(MRCA)) of a set of lineages. In an exponential growth scenario, we find that unless the product of population size (N) and growth rate (r) is at least approximately 10(5), the "pairwise comparison estimator" of T(MRCA) that derives from the star genealogy assumption has bias of 10-50%.

A simple dependence between protein evolution rate and the number of protein-protein interactions.

Background: It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions a protein has correlates negatively with their rates of evolution. However, the generality of this observation has recently been challenged. Here we examine the problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species.

Size matters: non-LTR retrotransposable elements and ectopic recombination in Drosophila.

The Drosophila melanogaster genome contains approximately 100 distinct families of transposable elements (TEs). In the euchromatic part of the genome, each family is present in a small number of copies (5-150 copies), with individual copies of TEs often present at very low frequencies in populations. This pattern is likely to reflect a balance between the inflow of TEs by transposition and the removal of TEs by natural selection.

Evolutionary rate in the protein interaction network.

High-throughput screens have begun to reveal the protein interaction network that underpins most cellular functions in the yeast Saccharomyces cerevisiae. How the organization of this network affects the evolution of the proteins that compose it is a fundamental question in molecular evolution. We show that the connectivity of well-conserved proteins in the network is negatively correlated with their rate of evolution.