Reduced SNP panels for genetic identification and introgression analysis in the dark honey bee (Apis mellifera mellifera)

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham's FST, an FST-based outlier test, Delta, informativeness (In), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs

Genetic integrity of the Dark European honey bee (Apis mellifera mellifera) from protected populations: a genome-wide assessment using SNPs and mtDNA sequence data

The recognition that the Dark European honey bee, Apis mellifera mellifera, is increasingly threatened in its native range has led to the establishment of conservation programmes and protected areas throughout western Europe. Previous molecular surveys showed that, despite management strategies to preserve the genetic integrity of A. m. mellifera, protected populations had a measurable component of their gene pool derived from commercial C-lineage honey bees. Here we used both sequence data from the tRNAleu-cox2 intergenic mtDNA region and a genome-wide scan, with over 1183 single nucleotide polymorphisms (SNPs), to assess genetic diversity and introgression levels in several protected populations of A. m. mellifera, which were then compared with samples collected from unprotected populations. MtDNA analysis of the protected populations revealed a single colony bearing a foreign haplotype, whereas SNPs showed varying levels of introgression ranging from virtually zero in Norway to about 14% in Denmark. Introgression overall was higher in unprotected (30%) than in protected populations (8%), and is reflected in larger SNP diversity levels of the former, although opposite diversity levels were observed for mtDNA. These results suggest that, despite controlled breeding, some protected populations still require adjustments to the management strategies to further purge foreign alleles, which can be identified by SNPs.Pint

Effect of linkage disequilibrium on inferences of population structure and introgression of iberian and black honey bees

Identification of population structure, a primary goal in population genetics, is easily performed because there is a number of methods available, implemented by user-friendly software packages. However, the user must be cautious when inferring population structure because spurious results may be obtained when there is strong linkage disequilibrium. With recent development of high-density SNPs we have now more power to interrogate the honey bee genome. However, the greater the number of loci genotyped the greater the chance of scoring loci that are linked. In addition, events such as population bottleneck, small effective population size, genetic drift, and admixture may also generate strong linkage disequilibrium. According to Kaeuffer et al. (2007), correlation rLD is the best way to deal with linkage disequilibrium. These authors recommend removing loci with rLD higher than 0.5 when inferring structure. In this study we used the GoldenGate Assay of Illumina to genotype over 1221 loci in individuals sampled from populations of A.m. iberiensis and A.m. mellifera. In this dataset we used the genetic distance between SNPs and rLD to test the effect of linkage in the number of clusters and the introgression level inferred by the clustering method implemented in the software STRUCTURE.Fundação para a Ciência e Tecnologi

Particle-unstable nuclei in the Hartree-Fock theory

Ground state energies and decay widths of particle unstable nuclei are calculated within the Hartree-Fock approximation by performing a complex scaling of the many-body Hamiltonian. Through this transformation, the wave functions of the resonant states become square integrable. The method is implemented with Skyrme effective interactions. Several Skyrme parametrizations are tested on four unstable nuclei: 10He, 12O, 26O and 28O.Comment: 5 pages, LaTeX, submitted to Phys. Rev. Let

Three-body Faddeev Calculation for 11Li with Separable Potentials

The halo nucleus $^{11}$Li is treated as a three-body system consisting of an inert core of $^{9}$Li plus two valence neutrons. The Faddeev equations are solved using separable potentials to describe the two-body interactions, corresponding in the n-$^{9}$Li subsystem to a p$_{1/2}$ resonance plus a virtual s-wave state. The experimental $^{11}$Li energy is taken as input and the $^{9}$Li transverse momentum distribution in $^{11}$Li is studied.Comment: 6 pages, RevTeX, 1 figur

Single-Proton Removal Reaction Study of 16B

The low-lying level structure of the unbound system $^{16}$B has been investigated via single-proton removal from a 35 MeV/nucleon $^{17}$C beam. The coincident detection of the beam velocity $^{15}$B fragment and neutron allowed the relative energy of the in-flight decay of $^{16}$B to be reconstructed. The resulting spectrum exhibited a narrow peak some 85 keV above threshold. It is argued that this feature corresponds to a very narrow ($\Gamma \ll$100 keV) resonance, or an unresolved multiplet, with a dominant $\pi (p_{3/2})^{-1} \otimes \nu (d_{5/2}^3)_{J=3/2^+}$ + $\pi (p_{3/2})^{-1} \otimes \nu (d_{5/2}^2,s_{1/2})_{J=3/2^+}$ configuration which decays by d-wave neutron emission.Comment: 16 pages, 5 figures, 1 table, submitted to Phys. Lett.

A novel SNP-based tool for estimating C-lineage introgression in the dark honey bee (Apis mellifera mellifera)

The natural distribution ofthe honeybee (Apis mellifera L.) hás been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apís mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained forthe fourassays combined (117 SNPs). The best compromise between accuracy ana genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation of introgression leveis to more effectively monitor and manage A. m. mellífera conservatories.info:eu-repo/semantics/publishedVersio

Breakup Reactions of 11Li within a Three-Body Model

We use a three-body model to investigate breakup reactions of 11Li (n+n+9Li) on a light target. The interaction parameters are constrained by known properties of the two-body subsystems, the 11Li binding energy and fragmentation data. The remaining degrees of freedom are discussed. The projectile-target interactions are described by phenomenological optical potentials. The model predicts dependence on beam energy and target, differences between longitudinal and transverse momentum distributions and provides absolute values for all computed differential cross sections. We give an almost complete series of observables and compare with corresponding measurements. Remarkably good agreement is obtained. The relative neutron-9Li p-wave content is about 40%. A p-resonance, consistent with measurements at about 0.5 MeV of width about 0.4 MeV, seems to be necessary. The widths of the momentum distributions are insensitive to target and beam energy with a tendency to increase towards lower energies. The transverse momentum distributions are broader than the longitudinal due to the diffraction process. The absolute values of the cross sections follow the neutron-target cross sections and increase strongly for beam energies decreasing below 100 MeV/u.Comment: 19 pages, 14 figures, RevTeX, psfig.st

Obstructive sleep apnea is underrecognized and underdiagnosed in patients undergoing bariatric surgery

The aim of this study was to evaluate prevalence of obstructive sleep apnea among patients undergoing bariatric surgery and the predictive value of various clinical parameters: body mass index (BMI), neck circumference (NC) and the Epworth Sleepiness Scale (ESS). We performed a prospective, multidisciplinary, single-center observational study including all patients on the waiting list for bariatric surgery between June 2009 and June 2010, irrespective of history or clinical findings. Patients visited our ENT outpatient clinic for patient history, ENT and general examination and underwent a full night polysomnography, unless performed previously. As much as 69.9% of the patients fulfilled the criteria for OSA (mean BMI 44.2 ± SD 6.4 kg/m2); 40.4% of the patients met the criteria for severe OSA. The regression models found BMI to be the best clinical predictor, while the ROC curve found the NC to be the most accurate predictor of the presence of OSA. The discrepancy of the results and the poor statistical power suggest that all three clinical parameters are inadequate predictors of OSA. In conclusion, in this large patient series, 69.9% of patients undergoing BS meet the criteria for OSA. More than 40% of these patients have severe OSA. A mere 13.3% of the patients were diagnosed with OSA before being placed on the waiting list for BS. On statistical analysis, increased neck circumference, BMI and the ESS were found to be insufficient predictors of the presence of OSA. Polysomnography is an essential component of the preoperative workup of patients undergoing BS. When OSA is found, specific perioperative measures are indicated