An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution

A large offspring-number diploid biparental multilocus population model of Moran type is our object of study. At each time step, a pair of diploid individuals drawn uniformly at random contributes offspring to the population. The number of offspring can be large relative to the total population size. Similar “heavily skewed” reproduction mechanisms have been recently considered by various authors (cf. e.g., Eldon and Wakeley 2006, 2008) and reviewed by Hedgecock and Pudovkin (2011). Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can coalesce only when in distinct individuals. A separation-of-timescales phenomenon is thus observed. A result of Möhle (1998) is extended to obtain convergence of the ancestral process to an ancestral recombination graph necessarily admitting simultaneous multiple mergers of ancestral lineages. The usual ancestral recombination graph is obtained as a special case of our model when the parents contribute only one offspring to the population each time. Due to diploidy and large offspring numbers, novel effects appear. For example, the marginal genealogy at each locus admits simultaneous multiple mergers in up to four groups, and different loci remain substantially correlated even as the recombination rate grows large. Thus, genealogies for loci far apart on the same chromosome remain correlated. Correlation in coalescence times for two loci is derived and shown to be a function of the coalescence parameters of our model. Extending the observations by Eldon and Wakeley (2008), predictions of linkage disequilibrium are shown to be functions of the reproduction parameters of our model, in addition to the recombination rate. Correlations in ratios of coalescence times between loci can be high, even when the recombination rate is high and sample size is large, in large offspring-number populations, as suggested by simulations, hinting at how to distinguish between different population models.     

Impacts of logging and conversion of rainforest to oil palm on the functional diversity of birds in Sundaland

Commercial selective logging and the conversion of primary and degraded forests to agriculture are the biggest threats to tropical biodiversity. Our understanding of the impacts of these disturbances and the resulting local extinctions on the functional roles performed by the remaining species is limited. We address this issue by examining functional diversity (FD), which quantifies a range of traits that affect a species' ecological role in a community as a single continuous metric. We calculated FD for birds across a gradient of disturbance from primary forest through intensively logged forest to oil palm plantations on previously forested land in Borneo, Southeast Asia, a hotspot of imperilled biodiversity. Logged rainforest retained similar levels of FD to unlogged rainforest, even after two logging rotations, but the conversion of logged forest to oil palm resulted in dramatic reductions in FD. The few remaining species in oil palm filled a disproportionately wide range of functional roles but showed very little clustering in terms of functional traits, suggesting that any further extinctions from oil palm would reduce FD even further. Determining the extent to which the changes we recorded were due to under‐utilization of resources within oil palm or a reduction in the resources present is an important next step. Nonetheless our study improves our understanding of the stability and resilience of functional diversity in these ecosystems and of the implications of land‐use changes for ecosystem functioning.     

丛枝菌根真菌对西瓜嫁接苗生长和根系防御性酶活性的影响

在温室盆栽条件下,研究丛枝菌根(AM)真菌地表球囊霉(Glomus versiforme)对连作土壤中西瓜自根苗和嫁接苗生长、根系膜透性、丙二醛(MDA)含量和防御性酶活性的影响.结果表明： 接种AM真菌能显著增加西瓜自根苗和嫁接苗的生物量,提高根系活力,降低根系膜透性和MDA含量.接种AM真菌的自根苗地上部鲜质量、地上部干质量和根系活力分别增加了57.6%、60.0%和142.1%,而接种AM真菌的嫁接苗分别增加了26.7%、28.0%和11.0%;自根苗（C）、嫁接苗（G）、接种AM真菌自根苗（C+M）和接种AM真菌嫁接苗（G+M）的根系细胞膜透性为C>G>C+M>G+M,根系MDA含量为C>G>G+M>C+M.接种AM真菌能提高西瓜自根苗和嫁接苗根系的苯丙氨酸解氨酶(PAL)、过氧化氢酶(CAT)、过氧化物酶(POD)、几丁质酶和β 1,3 葡聚糖酶活性,而且接种AM真菌的西瓜自根苗和嫁接苗根系POD、PAL和β-1,3-葡聚糖酶活性的峰值比不接种的提前2周出现.接种AM真菌能激活西瓜自根苗和嫁接苗与抗逆性有关的防御性酶反应,使根系对逆境产生快速反应,从而提高其抗连作障碍的能力.     

Practical considerations in the study of spectral analysis of discrete processes

Abstract

Clock hour independent groups of young female rats received a series of 3 alternate day intra‐articular injections of methylprednisolone acetate. All rats lost body weight, but the change was minimal when the injections were given in the late afternoon (‐30.8 g) vs the night (‐42.4 g, P < .02). The data imply that methylprednisolone acetate, which is designed to be locally active in joint spaces, can be absorbed into the circulation and that the rate of absorption is subject to circadian control.     

Effects of rotational and continuous grazing on herbage quality,feed intake and performance of sheep on a semi-arid grassland steppe

Compared to continuous grazing (CG), rotational grazing (RG) increases herbage production and thereby the resilience of grasslands to intensive grazing. Results on feed intake and animal performance, however, are contradictory. Hence, the objective of the study was to determine the effects of RG and CG on herbage mass, digestibility of ingested organic matter (dOM), organic matter intake (OMI) and live weight gain (LWG) of sheep in the Inner Mongolian steppe, China. During June–September 2005–2008, two 2-ha plots were used for each grazing system. In RG, plots were divided into four 0.5-ha paddocks that were grazed for 10 days each at a moderate stocking rate. Instead, CG sheep grazed the whole plots throughout the entire grazing season. At the beginning of every month, dOM was estimated from faecal crude protein concentration. Faeces excretion was determined using titanium dioxide in six sheep per plot. The animals were weighed every month to determine their LWG. Across the years, herbage mass did not differ between systems (p = 0.820). However, dOM, OMI and LWG were lower in RG than in CG (p ≤ 0.005). Thus, our study showed that RG does not improve herbage growth, feed intake and performance of sheep and suggests that stocking rates rather than management system determine the ecological sustainability of pastoral livestock systems in semi-arid environments.     

Phytotoxicity induced by Phragmites australis: an assessment of phenotypic and physiological parameters involved in germination process and growth of receptor plant

This study investigated the possible phytotoxicity induced by Phargmites australis on phenotypic and physiological parameters of recipient plants with identification of major inhibitors in the donor plant. This was achieved using aqueous extracts of different organs and root exudates of P. australis in laboratory and greenhouse experiments with Lactuca sativa as the model test plant. The observed reduced liquid imbibition and altered resource mobilization in seeds of L. sativa, in particular an insufficient carbohydrate supply, demonstrated that the onset of germination might be negatively affected by phytotoxicity. Dose-response studies pointed out that oxidative stress through reactive oxygen species production could potentially cause the observed germination and seedling growth reductions. The osmotic effects by mannitol solution on germination as well as growth and physiology at a level of ?0.57 and ?0.45 bar, respectively, demonstrated that the results from aqueous plant extracts were partially induced by the osmotic potential on and above those levels. Overall, the relative strength of inhibition on measured parameters was the highest in leaf extract, followed by rhizome, root, stem, and inflorescence. Root exudates of P. australis also had negative impacts by reducing germination and growth of plant. High-performance liquid chromatography (HPLC) analysis revealed gallic acid, a potent phytotoxin, as a major compound with an order of leaf >inflorescence>rhizome>root>stem.     

Potential impacts on ecosystem services of land use transitions to second‐generation bioenergy crops in GB

We present the first assessment of the impact of land use change (LUC) to second‐generation (2G) bioenergy crops on ecosystem services (ES) resolved spatially for Great Britain (GB). A systematic approach was used to assess available evidence on the impacts of LUC from arable, semi‐improved grassland or woodland/forest, to 2G bioenergy crops, for which a quantitative ‘threat matrix’ was developed. The threat matrix was used to estimate potential impacts of transitions to either Miscanthus, short‐rotation coppice (SRC, willow and poplar) or short‐rotation forestry (SRF). The ES effects were found to be largely dependent on previous land uses rather than the choice of 2G crop when assessing the technical potential of available biomass with a transition from arable crops resulting in the most positive effect on ES. Combining these data with constraint masks and available land for SRC and Miscanthus (SRF omitted from this stage due to lack of data), south‐west and north‐west England were identified as areas where Miscanthus and SRC could be grown, respectively, with favourable combinations of economic viability, carbon sequestration, high yield and positive ES benefits. This study also suggests that not all prospective planting of Miscanthus and SRC can be allocated to agricultural land class (ALC) ALC 3 and ALC 4 and suitable areas of ALC 5 are only minimally available. Beneficial impacts were found on 146 583 and 71 890 ha when planting Miscanthus or SRC, respectively, under baseline planting conditions rising to 293 247 and 91 318 ha, respectively, under 2020 planting scenarios. The results provide an insight into the interplay between land availability, original land uses, bioenergy crop type and yield in determining overall positive or negative impacts of bioenergy cropping on ecosystems services and go some way towards developing a framework for quantifying wider ES impacts of this important LUC.     

GAP promoter‐based fed‐batch production of highly bioactive core streptavidin by Pichia pastoris

Streptavidin is a homotetrameric protein binding the vitamin biotin and peptide analogues with an extremely high affinity, which leads to a large variety of applications. The biotin‐auxotrophic yeast Pichia pastoris has recently been identified as a suitable host for the expression of the streptavidin gene, allowing both high product concentrations and productivities. However, so far only methanol‐based expression systems have been applied, bringing about increased oxygen demand, strong heat evolution and high requirements for process safety, causing increased cost. Moreover, common methanol‐based processes lead to large proportions of biotin‐blocked binding sites of streptavidin due to biotin‐supplemented media. Targeting these problems, this paper provides strategies for the methanol‐free production of highly bioactive core streptavidin by P. pastoris under control of the constitutive GAP promoter. Complex were superior to synthetic production media regarding the proportion of biotin‐blocked streptavidin. The optimized, easily scalable fed‐batch process led to a tetrameric product concentration of up to 4.16 ± 0.11 µM of biotin‐free streptavidin and a productivity of 57.8 nM h^?1 based on constant glucose feeding and a successive shift of temperature and pH throughout the cultivation, surpassing the concentration in un‐optimized conditions by a factor of 3.4. Parameter estimation indicates that the optimized conditions caused a strongly increased accumulation of product at diminishing specific growth rates (μ ≈ D < 0.01 h^?1), supporting the strategy of feeding. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:855–864, 2016