The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu.

Wc prcscnt a novel methodology for identifying intcrnal iichvork performance characteristics baucd on cnd-to-end mullicnst measuretncnts. The mcthodology, solidly groiinded on statistical cstiination thcory, c a n bc uscd to clifiracterize the internal loss atid dciay lrrcliavior of a nctwork. Measurcnicnts on thc MI3anc havc been uscd tu validate thc approach in the case of Insscs. Extensive simulation experitncnts providc furihcr validaiion of the apprnacli, not only for losses, but also for delays. Wc also dcscribe our stratcgy for deploying the methodology on thc Intcrnct. This includcs the continued developmciit of the Naliorinl Internet Measurement hCrastriicture to support RTP-hascd cnd-to-cntl multicast ineasurcmciit~ sild the dcvclopnicnt of software tools tu analyze the traces. Once complete, this combincd softwarc/hardware inlrastriicturc will providc B scrvicc for understanding and forccasting tlic pcrformancc of the Internet.

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Historically, the Internet has been woefully under-measured and under-instrumented. The problem is only getting worse with the network's ever-increasing size. We discuss the goals and requirements for building a "measurement infrastructure" for the Internet, in which a collection of measurement "platforms" cooperatively measure the properties of Internet paths and clouds by exchanging test traffic among themselves. The key emphasis of the architecture, which forms the underpinnings of the National Internet Measurement Infrastructure (NIMI) project, is on tackling problems related to scale. Consequently, the architecture emphasizes decentralized control of measurements; strong authentication and security; mechanisms for both maintaining tight administrative control over who can perform what measurements using which platforms, and delegation of some forms of measurement as a site's measurement policy permits; and simple configuration and maintenance of platforms.