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The evolution of molecular quantitative traits, such as codon usage bias or base frequencies, can be explained as the result of mutational biases alone, or as the result of mutation and selection. Whereas mutation models can be investigated easily, realistic modelling of selection-directed genome evolution is analytically intractable, and numerical calculations require substantial computer resources. We investigated the evolution of optimal codon frequency under additive and multiplicative effects of selected linked codons. We show that additive selective effects of many linked sites cannot be effective in genomes when the number of selected sites is greater than the effective population size, a realistic assumption according to current molecular data. We then discuss the implications of these results for isochore evolution in vertebrates.

Abstract-To fully take advantage of high-speed networks while freeing CPU cycles for application processing, the industry is proposing new techniques relying on an extended role of the network interface card such as TCP Offload Engine and Remote Direct Memory Access. This paper presents an experimental study aimed at collecting the performance data needed to assess these techniques. This work is based on the emulation of an advanced network interface card plugged on the I/O bus. In the experimental setting, a processor of a partitioned SMP machine is dedicated to network processing. Achieving a faithful emulation of a network interface card is one of the main concerns and it is guiding the design of the Offload Engine software. This setting has the advantage of being flexible so that many different offload scenarios can be evaluated. Preliminary throughput results of an emulated TCP Offload Engine demonstrate a large benefit. The emulated TCP Offload Engine indeed yields 600 to 900% improvement while still relying on memory copies at the kernel boundary.

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