Noncoding regions underpin avian bill shape diversification at macroevolutionary scales [preprint]

Recent progress has been made in identifying genomic regions implicated in trait evolution on a microevolutionary scale in many species, but whether these are relevant over macroevolutionary time remains unclear. Here, we directly address this fundamental question using bird beak shape, a key evolutionary innovation linked to patterns of resource use, divergence and speciation, as a model trait. We integrate class-wide geometric-morphometric analyses with evolutionary sequence analyses of 10,322 protein coding genes as well as 229,001 genomic regions spanning 72 species. We identify 1,434 protein coding genes and 39,806 noncoding regions for which molecular rates were significantly related to rates of bill shape evolution. We show that homologs of the identified protein coding genes as well as genes in close proximity to the identified noncoding regions are involved in craniofacial embryo development in mammals. They are associated with embryonic stem cells pathways, including BMP and Wnt signalling, both of which have repeatedly been implicated in the morphological development of avian beaks. This suggests that identifying genotype-phenotype association on a genome wide scale over macroevolutionary time is feasible. While the coding and noncoding gene sets are associated with similar pathways, the actual genes are highly distinct, with significantly reduced overlap between them and bill-related phenotype associations specific to noncoding loci. Evidence for signatures of recent diversifying selection on our identified noncoding loci in Darwin finch populations further suggests that regulatory rather than coding changes are major drivers of morphological diversification over macroevolutionary times

Boron-enhanced diffusion of boron from ultralow-energy boron implantation

The authors have investigated the diffusion enhancement mechanism of BED (boron enhanced diffusion), wherein the boron diffusivity is enhanced three to four times over the equilibrium diffusivity at 1,050 C in the proximity of a silicon layer containing a high boron concentration. It is shown that BED is associated with the formation of a fine-grain polycrystalline silicon boride phase within an initially amorphous Si layer having a high B concentration. For 0.5 keV B{sup +}, the threshold implantation dose which leads to BED lies between 3 {times} 10{sup 14} and of 1 {times} 10{sup 15}/cm{sup {minus}2}. Formation of the shallowest possible junctions by 0.5 keV B{sup +} requires that the implant dose be kept lower than this threshold

Vacancy supersaturations produced by high-energy ion implantation

A new technique for detecting the vacancy clusters produced by high-energy ion implantation into silicon is proposed and tested. This technique takes advantage of the fact that metal impurities, such as Au, are gettered near one-half of the projected range ({1/2}R{sub p}) of MeV implants. The vacancy clustered region produced by a 2 MeV Si{sup +} implant into silicon has been labeled with Au diffused in from the front surface. The trapped Au was detected by Rutherford backscattering spectrometry (RBS) to profile the vacancy clusters. Cross section transmission electron microscopy (XTEM) analysis shows that the Au in the region of vacancy clusters is in the form of precipitates. By annealing MeV implanted samples prior to introduction of the Au, changes in the defect concentration within the vacancy clustered region were monitored as a function of annealing conditions

Boron-enhanced-diffusion of boron: The limiting factor for ultra-shallow junctions

Reducing implant energy is an effective way to eliminate transient enhanced diffusion (TED) due to excess interstitials from the implant. It is shown that TED from a fixed Si dose implanted at energies from 0.5 to 20 keV into boron doping-superlattices decreases linearly with decreasing Si ion range, virtually disappearing at sub-keV energies. However, for sub-keV B implants diffusion remains enhanced and x{sub j} is limited to {ge} 100 nm at 1,050 C. The authors term this enhancement, which arises in the presence of B atomic concentrations at the surface of {approx} 6%, Boron-Enhanced-Diffusion (BED)

Front-end process modeling in silicon

Front-end processing mostly deals with technologies associated to junction formation in semiconductor devices. Ion implantation and thermal anneal models are key to predict active dopant placement and activation. We review the main models involved in process simulation, including ion implantation, evolution of point and extended defects, amorphization and regrowth mechanisms, and dopant-defect interactions. Hierarchical simulation schemes, going from fundamental calculations to simplified models, are emphasized in this Colloquium. Although continuum modeling is the mainstream in the semiconductor industry, atomistic techniques are starting to play an important role in process simulation for devices with nanometer size features. We illustrate in some examples the use of atomistic modeling techniques to gain insight and provide clues for process optimization