Emission Spectrum of a Dipole in a Semi-infinite Periodic Dielectric Structure: Effect of the Boundary

The emission spectrum of a dipole embedded in a semi-infinite photonic crystal is calculated. For simplicity we study the case in which the dielectric function is sinusoidally modulated only along the direction perpendicular to the boundary surface plane. In addition to oscillations of the emission rate with the distance of the dipole from the interface we also observed that the shape of the emission spectrum srongly depends on the \em initial \em phase of the dielectric modulation. When the direction of light propagation inside the periodic structure is not normal to the boundary surface plane we observed aditional singularities in the emission spectrum, which arise due to different angle-dependence of the Bragg stop-band for $TE$ and $TM$ polarizations.Comment: 14 pages, 6 figures, to appear in Phys Rev

Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations

In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island South-East Asia (ISEA). A previous study revealed signatures of interspecific admixture between these Sus species (Genome biology,14, 2013, R107). However, the timing, directionality and extent of this admixture remain unknown. Here, we use a likelihood-based model comparison to more finely resolve this admixture history and test whether it was mediated by humans or occurred naturally. Our analyses suggest that interspecific admixture between Sunda-shelf species was most likely asymmetric and occurred long before the arrival of humans in the region. More precisely, we show that these species diverged during the late Pliocene but around 23% of their genomes have been affected by admixture during the later Pleistocene climatic transition. In addition, we show that our method provides a significant improvement over D-statistics which are uninformative about the direction of admixture

A simple formula for the L-gap width of a face-centered-cubic photonic crystal

The width $\triangle_L$ of the first Bragg's scattering peak in the (111) direction of a face-centered-cubic lattice of air spheres can be well approximated by a simple formula which only involves the volume averaged $\epsilon$ and $\epsilon^2$ over the lattice unit cell, $\epsilon$ being the (position dependent) dielectric constant of the medium, and the effective dielectric constant $\epsilon_{eff}$ in the long-wavelength limit approximated by Maxwell-Garnett's formula. Apparently, our formula describes the asymptotic behaviour of the absolute gap width $\triangle_L$ for high dielectric contrast $\delta$ exactly. The standard deviation $\sigma$ steadily decreases well below 1% as $\delta$ increases. For example $\sigma< 0.1$ for the sphere filling fraction $f=0.2$ and $\delta\geq 20$. On the interval $\delta\in(1,100)$, our formula still approximates the absolute gap width $\triangle_L$ (the relative gap width $\triangle_L^r$) with a reasonable precision, namely with a standard deviation 3% (4.2%) for low filling fractions up to 6.5% (8%) for the close-packed case. Differences between the case of air spheres in a dielectric and dielectric spheres in air are briefly discussed.Comment: 13 pages, 4 figs., RevTex, two references added. For more info see http://www.amolf.nl/external/wwwlab/atoms/theory/index.htm

Genetic consequences of long‐term small effective population size in the critically endangered pygmy hog

Increasing human disturbance and climate change have a major impact on habitat integrity and size, with far‐reaching consequences for wild fauna and flora. Specifically, population decline and habitat fragmentation result in small, isolated populations. To what extend different endangered species can cope with small population size is still largely unknown. Studies on the genomic landscape of these species can shed light on past demographic dynamics and current genetic load, thereby also providing guidance for conservation programs. The pygmy hog (Porcula salvania) is the smallest and rarest wild pig in the world, with current estimation of only a few hundred living in the wild. Here, we analyzed whole‐genome sequencing data of six pygmy hogs, three from the wild and three from a captive population, along with 30 pigs representing six other Suidae. First, we show that the pygmy hog had a very small population size with low genetic diversity over the course of the past ~1 million years. One indication of historical small effective population size is the absence of mitochondrial variation in the six sequenced individuals. Second, we evaluated the impact of historical demography. Runs of homozygosity (ROH) analysis suggests that the pygmy hog population has gone through past but not recent inbreeding. Also, the long‐term, extremely small population size may have led to the accumulation of harmful mutations suggesting that the accumulation of deleterious mutations is exceeding purifying selection in this species. Thus, care has to be taken in the conservation program to avoid or minimize the potential for further inbreeding depression, and guard against environmental changes in the future.FWN – Publicaties zonder aanstelling Universiteit Leide

Angular redistribution of near-infrared emission from quantum dots in 3D photonic crystals

We study the angle-resolved spontaneous emission of near-infrared light sources in 3D photonic crystals over a wavelength range from 1200 to 1550 nm. To this end PbSe quantum dots are used as light sources inside titania inverse opal photonic crystals. Strong deviations from the Lambertian emission profile are observed. An attenuation of 60 % is observed in the angle dependent radiant flux emitted from the samples due to photonic stop bands. At angles that correspond to the edges of the stop band the emitted flux is increased by up to 34 %. This increase is explained by the redistribution of Bragg-diffracted light over the available escape angles. The results are quantitatively explained by an expanded escape-function model. This model is based on diffusion theory and adapted to photonic crystals using band structure calculations. Our results are the first angular redistributions and escape functions measured at near-infrared, including telecom, wavelengths. In addition, this is the first time for this model to be applied to describe emission from samples that are optically thick for the excitation light and relatively thin for the photoluminesence light.Comment: 24 pages, 8 figures (current format = single column, double spaced

Signatures of Selection in the Genomes of Commercial and Non-Commercial Chicken Breeds

Identifying genomics regions that are affected by selection is important to understand the domestication and selection history of the domesticated chicken, as well as understanding molecular pathways underlying phenotypic traits and breeding goals. While whole-genome approaches, either high-density SNP chips or massively parallel sequencing, have been successfully applied to identify evidence for selective sweeps in chicken, it has been difficult to distinguish patterns of selection and stochastic and breed specific effects. Here we present a study to identify selective sweeps in a large number of chicken breeds (67 in total) using a high-density (58 K) SNP chip. We analyzed commercial chickens representing all major breeding goals. In addition, we analyzed non-commercial chicken diversity for almost all recognized traditional Dutch breeds and a selection of representative breeds from China. Based on their shared history or breeding goal we in silico grouped the breeds into 14 breed groups. We identified 396 chromosomal regions that show suggestive evidence of selection in at least one breed group with 26 of these regions showing strong evidence of selection. Of these 26 regions, 13 were previously described and 13 yield new candidate genes for performance traits in chicken. Our approach demonstrates the strength of including many different populations with similar, and breed groups with different selection histories to reduce stochastic effects based on single populations

Free energy of colloidal particles at the surface of sessile drops

The influence of finite system size on the free energy of a spherical particle floating at the surface of a sessile droplet is studied both analytically and numerically. In the special case that the contact angle at the substrate equals $\pi/2$ a capillary analogue of the method of images is applied in order to calculate small deformations of the droplet shape if an external force is applied to the particle. The type of boundary conditions for the droplet shape at the substrate determines the sign of the capillary monopole associated with the image particle. Therefore, the free energy of the particle, which is proportional to the interaction energy of the original particle with its image, can be of either sign, too. The analytic solutions, given by the Green's function of the capillary equation, are constructed such that the condition of the forces acting on the droplet being balanced and of the volume constraint are fulfilled. Besides the known phenomena of attraction of a particle to a free contact line and repulsion from a pinned one, we observe a local free energy minimum for the particle being located at the drop apex or at an intermediate angle, respectively. This peculiarity can be traced back to a non-monotonic behavior of the Green's function, which reflects the interplay between the deformations of the droplet shape and the volume constraint.Comment: 24 pages, 19 figure

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

Background Copy number variable regions (CNVRs) can result in drastic phenotypic differences and may therefore be subject to selection during domestication. Studying copy number variation in relation to domestication is highly relevant in pigs because of their very rich natural and domestication history that resulted in many different phenotypes. To investigate the evolutionary dynamic of CNVRs, we applied read depth method on next generation sequence data from 16 individuals, comprising wild boars and domestic pigs from Europe and Asia. Results We identified 3,118 CNVRs with an average size of 13 kilobases comprising a total of 39.2 megabases of the pig genome and 545 overlapping genes. Functional analyses revealed that CNVRs are enriched with genes related to sensory perception, neurological process and response to stimulus, suggesting their contribution to adaptation in the wild and behavioral changes during domestication. Variations of copy number (CN) of antimicrobial related genes suggest an ongoing process of evolution of these genes to combat food-borne pathogens. Likewise, some genes related to the omnivorous lifestyle of pigs, like genes involved in detoxification, were observed to be CN variable. A small portion of CNVRs was unique to domestic pigs and may have been selected during domestication. The majority of CNVRs, however, is shared between wild and domesticated individuals, indicating that domestication had minor effect on the overall diversity of CNVRs. Also, the excess of CNVRs in non-genic regions implies that a major part of these variations is likely to be (nearly) neutral. Comparison between different populations showed that larger populations have more CNVRs, highlighting that CNVRs are, like other genetic variation such as SNPs and microsatellites, reflecting demographic history rather than phenotypic diversity. Conclusion CNVRs in pigs are enriched for genes related to sensory perception, neurological process, and response to stimulus. The majority of CNVRs ascertained in domestic pigs are also variable in wild boars, suggesting that the domestication of the pig did not result in a change in CNVRs in domesticated pigs. The majority of variable regions were found to reflect demographic patterns rather than phenotypic

Genome sequencing reveals fine scale diversification and reticulation history during speciation in Sus

Background Elucidating the process of speciation requires an in-depth understanding of the evolutionary history of the species in question. Studies that rely upon a limited number of genetic loci do not always reveal actual evolutionary history, and often confuse inferences related to phylogeny and speciation. Whole-genome data, however, can overcome this issue by providing a nearly unbiased window into the patterns and processes of speciation. In order to reveal the complexity of the speciation process, we sequenced and analyzed the genomes of 10 wild pigs, representing morphologically or geographically well-defined species and subspecies of the genus Sus from insular and mainland Southeast Asia, and one African common warthog. Results Our data highlight the importance of past cyclical climatic fluctuations in facilitating the dispersal and isolation of populations, thus leading to the diversification of suids in one of the most species-rich regions of the world. Moreover, admixture analyses revealed extensive, intra- and inter-specific gene-flow that explains previous conflicting results obtained from a limited number of loci. We show that these multiple episodes of gene-flow resulted from both natural and human-mediated dispersal. Conclusions Our results demonstrate the importance of past climatic fluctuations and human mediated translocations in driving and complicating the process of speciation in island Southeast Asia. This case study demonstrates that genomics is a powerful tool to decipher the evolutionary history of a genus, and reveals the complexity of the process of speciation

The development and characterization of a 60K SNP chip for chicken

<p>Abstract</p> <p>Background</p> <p>In livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success rate of the SNP genotyping assay, the distribution of the SNP across the genome and the minor allele frequencies (MAF) of the SNPs used are extremely important.</p> <p>Results</p> <p>We describe the design of a moderate density (60k) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at high to medium minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two micro-chromosomes not covered by the current genome assembly.</p> <p>Conclusions</p> <p>The high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence (NGS) technology for the SNP identification and selection step. The identification of SNPs from sequence contigs derived from NGS sequencing resulted in improved coverage of the chicken genome and the construction of two new linkage groups most likely representing two chicken micro-chromosomes.</p