Leveraging whole genome sequencing data for demographic inference with approximate Bayesian computation

Accounting for historical demographic features, such as the strength and timing of gene flow and divergence times between closely related lineages, is vital for many inferences in evolutionary biology. Approximate Bayesian computation (ABC) is one method commonly used to estimate demographic parameters. However, the DNA sequences used as input for this method, often microsatellites or RADseq loci, usually represent a small fraction of the genome. Whole genome sequencing (WGS) data, on the other hand, have been used less often with ABC, and questions remain about the potential benefit of, and how to best implement, this type of data; we used pseudo‐observed data sets to explore such questions. Specifically, we addressed the potential improvements in parameter estimation accuracy that could be associated with WGS data in multiple contexts; namely, we quantified the effects of (a) more data, (b) haplotype‐based summary statistics, and (c) locus length. Compared with a hypothetical RADseq data set with 2.5 Mbp of data, using a 1 Gbp data set consisting of 100 Kbp sequences led to substantial gains in the accuracy of parameter estimates, which was mostly due to haplotype statistics and increased data. We also quantified the effects of including (a) locus‐specific recombination rates, and (b) background selection information in ABC analyses. Importantly, assuming uniform recombination or ignoring background selection had a negative effect on accuracy in many cases. Software and results from this method validation study should be useful for future demographic history analyses.     

Social Reinforcement Delays in Free-Flying Honey Bees (Apis mellifera L.)

Free-flying honey bees (Apis mellifera L.) reactions were observed when presented with varying schedules of post-reinforcement delays of 0 s, 300 s, or 600 s. We measured inter-visit-interval, response length, inter-response-time, and response rate. Honey bees exposed to these post-reinforcement delay intervals exhibit one of several patterns compared to groups not encountering delays, and had longer inter-visit-intervals. We observed no group differences in inter-response time. Honey bees with higher response rates tended to not finish the experiment. The removal of the delay intervals increased response rates for those subjects that completed the trials.     

β-adrenoceptors in human tracheal smooth muscle: characteristics of binding and relaxation

Specific binding of [¹²⁵I]-(−)-cyanopindolol to human tracheal smooth muscle membranes was saturable, stereo-selective and of high affinity (K_d=5.3±0.9 pmol/l and R_T=78±7fmol/g tissue). The β₁-selective antagonists atenolol and LK 203-030 inhibited specific [¹²⁵I]-(−)-cyanopindolol binding according to a one binding site model with low affinity in nearly all subjects, pointing to a homogeneous β₂-adrenoceptor population. In one subject using LK 203-030 a small β-adrenoceptor subpopulation could be demonstrated. The beta-mimetics isoprenaline, fenoterol, salbutamol and terbutaline recognized high and low affinity agonist binding sites. Isoprenaline's pK_H- and pK_L- values for the high and low affinity sites were 8.0±0.2 and 5.9±0.3 respectively. In functional experiments isoprenaline relaxed tracheal smooth muscle strips having intrinsic tone with a pD₂-value of 6.63±0.19.     

Methods of hatching the eggs and rearing the fundatrices of the English grain aphid, Sitobion avenae

Several methods for hatching the eggs and rearing individuals of the first generation (fundatrices) of Sitobion avenae were investigated. The most successful methods were incubation of the eggs on grass seedlings at 2°C and rearing the fundatrices on grass seedlings (overall survival 66%) and incubation of the eggs in plastic boxes at 2°C and rearing the fundatrices on wheat seedlings (overall survival 62%).

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Résumé L'éclosion des oeufs de S. avenae peut être induite par le transfert à 10°C ou 12°C, après une incubation de 75–120 jours à 2°C. Le pourcentage le plus élevé d'éclosions a été obtenu quand les oeufs avaient incubé pendant 100 à 110 jours à 2°C (67% at 71.5% respectivement) dans des petites boîtes de plastique, ou pendant 100 jours à 2°C sur des pousses de graminées (73.5%). Si les oeufs sont pondus sur blé, la plante ne peut pas tolérer la période d'incubation, mais cet obstacle peut être surmonté en obligeant les ovipares à pondre leurs oeufs sur de pousses de graminées, comme Poa annua, hôte convenable pour les fondatrices. Les ovipares peuvent aussi pondre sans difficultés sur autre chose que des végétaux, et des récipients peuvent ètre mis à incuber sans contenir du matériel végétal.

     

Localization and cloning of Xp21 deletion breakpoints involved in muscular dystrophy

Summary Twenty-nine deletion breakpoints were mapped in 220 kb of the DXS164 locus relative to potential exons of the Duchenne and Becker muscular dystrophy gene. Four deletion junction fragments were isolated to acquire outlying Xp21 loci on both the terminal and centromere side of the DXS164 locus. The junction loci were used for chromosome walking, searches for DNA polymorphisms, and mapping against deletion and translocation breakpoints. Forty-four unrelated deletions were analyzed using the junction loci as hybridization probes to map the endpoints between cloned Xp21 loci. DNA polymorphisms from the DXS164 and junction loci were used to follow the segregation of a mutation in a family that represents a recombinant. Both the physical and genetic data point to a very large size for this X-linked muscular dystrophy locus.     

Influence of oxygen and substrate supply on the metabolism of Candida maltosa during cultivation on n-alkanes

Summary The influence of different states of oxygen and alkane substrate supply on the metabolism of Candida maltosa during cultivation on n-alkanes has been investigated. At sufficient oxygen and substrate supply a nearly equimolar ratio between the formation of biomass and alkane oxidation was observed. About 45% of the carbon source utilized was incorporated into the biomass. Strong oxygen limitation decreased protein formation and carbon incorporation into the biomass with a simultaneous increase in CO₂ formation, whereas periodic changes of oxygen supply only caused a decrease in carbon incorporation into the biomass and an increase in CO₂ formation. During cultivation in the presence of an inert hydrocarbon (pristane) it was found that carbon limitation and oxygen saturation diminished the formation of total and nitrogen-containing biomass, whereas carbon and oxygen limitation reduced the formation of total biomass.Offprint requests to: P. Riege     

5,6,7,8-Tetrahydromethanopterin-dependent enzymes involved in methanogenesis

Abstract In the process of methanogenesis, 5,6,7,8-tetrahydromethanopterin (H₄MPT) is the carrier of the C₁ unit at the formyl through methyl state of reduction. By the transfer of a formyl group from formylmethanofuran, 5-formyl- and 10-formyl-H₄MPT are formed in hydrogenotrophic and methylotrophic organisms, respectively. Cyclohydrolysis of the 5- and 10-formyl derivatives then yields 5,10-methenyl-H₄MPT, which is reduced in two subsequent coenzyme F₄₂₀-dependent reactions to 5-methyl-H₄MPT. Following the transfer of the methyl group to coenzyme M, the substrate of the terminal step in methanogenesis, methylcoenzyme M, is produced. In this paper properties of the enzymes catalyzing the individual H₄MPT-dependent reactions are discussed.