Polyploidy breaks speciation barriers in Australian burrowing frogs Neobatrachus

Polyploidy has played an important role in evolution across the tree of life but it is still unclear how polyploid lineages may persist after their initial formation. While both common and well-studied in plants, polyploidy is rare in animals and generally less understood. The Australian burrowing frog genus Neobatrachus is comprised of six diploid and three polyploid species and offers a powerful animal polyploid model system. We generated exome-capture sequence data from 87 individuals representing all nine species of Neobatrachus to investigate species-level relationships, the origin and inheritance mode of polyploid species, and the population genomic effects of polyploidy on genus-wide demography. We describe rapid speciation of diploid Neobatrachus species and show that the three independently originated polyploid species have tetrasomic or mixed inheritance. We document higher genetic diversity in tetraploids, resulting from widespread gene flow between the tetraploids, asymmetric inter-ploidy gene flow directed from sympatric diploids to tetraploids, and isolation of diploid species from each other. We also constructed models of ecologically suitable areas for each species to investigate the impact of climate on differing ploidy levels. These models suggest substantial change in suitable areas compared to past climate, which correspond to population genomic estimates of demographic histories. We propose that Neobatrachus diploids may be suffering the early genomic impacts of climate-induced habitat loss, while tetraploids appear to be avoiding this fate, possibly due to widespread gene flow. Finally, we demonstrate that Neobatrachus is an attractive model to study the effects of ploidy on the evolution of adaptation in animals

Phylogenomics and analysis of shared genes suggest a single transition to mutualism in Wolbachia of nematodes

Wolbachia, endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis, revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event

Algorithms for the scaling toward nanometer VLSI physical synthesis

Along the history of Very Large Scale Integration (VLSI), we have successfully scaled down the size of transistors, scaled up the speed of integrated circuits (IC) and the number of transistors in a chip - these are just a few examples of our achievement in VLSI scaling. It is projected to enter the nanometer (timing estimation and buffer planning for global routing and other early stages such as floorplanning. A novel path based buffer insertion scheme is also included, which can overcome the weakness of the net based approaches. Part-2 Circuit clustering techniques with the application in Field-Programmable Gate Array (FPGA) technology mapping The problem of timing driven n-way circuit partitioning with application to FPGA technology mapping is studied and a hierarchical clustering approach is presented for the latest multi-level FPGA architectures. Moreover, a more general delay model is included in order to accurately characterize the delay behavior of the clusters and circuit elements

Incorporating Physical Information into Clustering for FPGAs

The traditional approach to FPGA clustering and CLB-level placement has been shown to yield significantly worse overall placement quality than approaches which allow BLEs to move during placement. In practice, however, modern FPGA architectures require computationally-expensive Design Rule Checks (DRC) which render BLE-level placement impractical. This thesis research addresses this problem by proposing a novel clustering framework that produces better initial clusters that help to reduce the dependence on BLE-level placement. The work described in this dissertation includes: (1) a comparison of various clustering algorithms used for FPGAs, (2) the introduction of a novel hybridized clustering framework for timing-driven FPGA clustering, (3) the addition of physical information to make better clusters, (4) a comparison of the implemented approaches to known clustering tools, and (5) the implementation and evaluation of cluster improvement heuristics. The proposed techniques are quantified across accepted benchmarks and show that the implemented DPack produces results with 16% less wire length, 19% smaller minimum channel widths, and 8% less critical delay, on average, than known academic tools. The hybridized approach, HDPack, is found to achieve 21% less wire length, 24% smaller minimum channel widths, and 6% less critical delay, on average