Single-crystal silicon nanowires with diameters approaching molecular dimensions were synthesized using gold nanocluster-catalyzed 1D growth. High-resolution transmission electron microscopy studies show that silicon nanowires grown with silane reactant in hydrogen are single crystal with little or no visible amorphous oxide down to diameters as small as 3 nm. Structural characterization of a large number of samples shows that the smallest-diameter nanowires grow primarily along the 〈110〉 direction, whereas larger nanowires grow along the 〈111〉 direction. In addition, cross-sectional transmission electron microscopy was used to address the importance of surface energetics in determining the growth direction of the smallest nanowires. The ability to prepare well-defined molecular-scale single-crystal silicon nanowires opens up new opportunities for both fundamental studies and nanodevice applications.

Anthrax, caused by the bacterium Bacillus anthracis, is a disease of historical and current importance that is found throughout the world. The basis of its historical transmission is anecdotal and its true global population structure has remained largely cryptic. Seven diverse B. anthracis strains were whole-genome sequenced to identify rare single nucleotide polymorphisms (SNPs), followed by phylogenetic reconstruction of these characters onto an evolutionary model. This analysis identified SNPs that define the major clonal lineages within the species. These SNPs, in concert with 15 variable number tandem repeat (VNTR) markers, were used to subtype a collection of 1,033 B. anthracis isolates from 42 countries to create an extensive genotype data set. These analyses subdivided the isolates into three previously recognized major lineages (A, B, and C), with further subdivision into 12 clonal sub-lineages or sub-groups and, finally, 221 unique MLVA15 genotypes. This rare genomic variation was used to document the evolutionary progression of B. anthracis and to establish global patterns of diversity. Isolates in the A lineage are widely dispersed globally, whereas the B and C lineages occur on more restricted spatial scales. Molecular clock models based upon genome-wide synonymous substitutions indicate there was a massive radiation of the A lineage that occurred in the mid-Holocene (3,064–6,127 ybp). On more recent temporal scales, the global population structure of B. anthracis reflects colonial-era importation of specific genotypes from the Old World into the New World, as well as the repeated industrial importation of diverse genotypes into developed countries via spore-contaminated animal products. These findings indicate humans have played an important role in the evolution of anthrax by increasing the proliferation and dispersal of this now global disease. Finally, the value of global genotypic analysis for investigating bioterrorist-mediated outbreaks of anthrax is demonstrated.

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Phylogenetic reconstruction using molecular data is often subject to homoplasy, leading to inaccurate conclusions about phylogenetic relationships among operational taxonomic units. Compared with other molecular markers, single-nucleotide polymorphisms (SNPs) exhibit extremely low mutation rates, making them rare in recently emerged pathogens, but they are less prone to homoplasy and thus extremely valuable for phylogenetic analyses. Despite their phylogenetic potential, ascertainment bias occurs when SNP characters are discovered through biased taxonomic sampling; by using whole-genome comparisons of five diverse strains of Bacillus anthracis to facilitate SNP discovery, we show that only polymorphisms lying along the evolutionary pathway between reference strains will be observed. We illustrate this in theoretical and simulated data sets in which complex phylogenetic topologies are reduced to linear evolutionary models. Using a set of 990 SNP markers, we also show how divergent branches in our topologies collapse to single points but provide accurate information on internodal distances and points of origin for ancestral clades. These data allowed us to determine the ancestral root of B. anthracis, showing that it lies closer to a newly described ''C'' branch than to either of two previously described ''A'' or ''B'' branches. In addition, subclade rooting of the C branch revealed unequal evolutionary rates that seem to be correlated with ecological parameters and strain attributes. Our use of nonhomoplastic whole-genome SNP characters allows branch points and clade membership to be estimated with great precision, providing greater insight into epidemiological, ecological, and forensic questions. T he discovery method used to find nonhomoplastic molecular characters can have a great impact on subsequent phylogenetic analyses (1). ''Discovery bias'' will most likely be encountered when polymorphic characters are rare and extraordinary means (i.e., whole-genome sequencing) are necessary to find them. In such cases, only a small subset of the target organisms can be exhaustively examined for genetic differences. When these polymorphisms are assayed across a more extensive and diverse panel of strains, the phylogenetic topology will be impacted greatly by the original choices of strains used for character discovery. Consider a six-taxon dendrogram (Fig. 1) in which nonhomoplastic polymorphic characters are discovered by exhaustive comparisons of two taxa. Mutational events that create character differences on the evolutionary path connecting the two taxa will be discovered, but characters on tangential (i.e., secondary) branches will not. Subsequent character-state determination in all taxa will accurately place them onto a linear phylogeny but will underrepresent the taxonomic complexity by eliminating secondary branching. If the initial character discovery is between two closely related taxa, large diverse clades will be reduced to a single point on a short linear dendrogram (Fig. 1B). This theoretical model assu...

We examined the effects of habitat discontinuities on gene flow among puma (Puma concolor) populations across the southwestern USA. Using 16 microsatellite loci, we genotyped 540 pumas sampled throughout the states of Utah, Colorado, Arizona, and New Mexico, where a high degree of habitat heterogeneity provides for a wide range of connective habitat configurations between subpopulations. We investigated genetic structuring using complementary individual- and population-based analyses, the latter employing a novel technique to geographically cluster individuals without introducing investigator bias. The analyses revealed genetic structuring at two distinct scales. First, strikingly strong differentiation between northern and southern regions within the study area suggests little migration between them. Second, within each region, gene flow appears to be strongly limited by distance, particularly in the presence of habitat barriers such as open desert and grasslands. Northern pumas showed both reduced genetic diversity and greater divergence from a hypothetical ancestral population based on Bayesian clustering analyses, possibly reflecting a post-Pleistocene range expansion. Bayesian clustering results were sensitive to sampling density, which may complicate inference of numbers of populations when using this method. The results presented here build on those of previous studies, and begin to complete a picture of how different habitat types facilitate or impede gene flow among puma populations.