Population dynamics of GC-changing mutations in humans and great apes

The nucleotide composition of the genome is a balance between the origin and fixation rates of different mutations. For example, it is well-known that transitions occur more frequently than transversions, particularly at CpG sites. Differences in fixation rates of mutation types are less explored. Specifically, recombination-associated GC-biased gene conversion (gBGC) may differentially impact GC-changing mutations, due to differences in their genomic distributions and efficiency of mismatch repair mechanisms. Given that recombination evolves rapidly across species, we explore gBGC of different mutation types across human populations and great ape species. We report a stronger correlation between segregating GC frequency and recombination for transitions than for transversions. Notably, CpG transitions are most strongly affected by gBGC in humans and chimpanzees. We show that the overall strength of gBGC is generally correlated with effective population sizes in humans, with some notable exceptions, such as a stronger effect of gBGC on non-CpG transitions in populations of European descent. Furthermore, species of the Gorilla and Pongo genus have a greatly reduced gBGC effect on CpG sites. We also study the dependence of gBGC dynamics on flanking nucleotides and show that some mutation types evolve in opposition to the gBGC expectation, likely due to the hypermutability of specific nucleotide contexts. Our results highlight the importance of different gBGC dynamics experienced by GC-changing mutations and their impact on nucleotide composition evolution.     

A mechanistic model for partial preferences

Classic prey optimal foraging model assumes that individual predators are globally omniscient; that is, they have exact knowledge of prey population densities in the environment. This study examines a spatially explicit individual-based model of a one-predator two-prey system where individual predators are assumed to be omniscient only locally, i.e., to know prey population densities only in the range of their perception. Due to local variations in prey numbers, the probability of acceptance of less profitable prey shifts from the zero-one rule to a gradually decreasing function, for which an explicit formula is derived, giving way to partial preferences. A corresponding predator functional response to more profitable prey is shown to have a sigmoid-like form.     

Thermocline deepening and mixing alter zooplankton phenology,biomass and body size in a whole‐lake experiment

相似文献   

Nutrients and antinutrient constituents of Amaranthus caudatus L. Cultivated on different soils

This study investigated variations in the concentration of nutrients, antinutrients and mineral content of Amaranthus caudatus harvested from different soil types at various stages of maturity. Four out the five soils namely; sandy clay loam, silty clay loam, clayey loam and loam were experimentally formulated from primary particles of silt, clay and sand in line with the United State Department of Agriculture’s (USDA) soil triangle protocol. The unfractionated soil was used as the control. After harvesting at pre-flowering (61 days after planting), flowering (71 days after planting) and post-flowering (91 days after planting) stages, nutrient and antinutrient analyses were carried out following Association of Official Analytical Chemists (AOAC) and other referenced methods while the Inductively Coupled Plasma- Optical Emission Spectrometer was used to determine mineral compositions of the plant samples. The results of the study revealed that particle size and physicochemical properties of the soil influenced the number of minerals deposited in plant tissues. It was further observed that the nutritional properties of the plant change as plant ages. For an optimal yield of vitamins A and E, clayey loam proved to be the best soil particularly when A. caudatus is harvested before flowering but for vitamin C, sandy clayey loam yielded the highest output at the same stage. Similarly, clayey loam and loam soils yielded the highest proximate compositions at flowering and pre-flowering; however, mineral elements (micro and macro) were highest in control and loam soils.     

Diet composition of post-metamorphic bullfrogs (Rana catesbeiana) in the Zhoushan archipelago, Zhejiang Province, China

Bullfrogs (Rana catesbeiana) are listed as one of the 100 worst invasive alien species in the world. They are generalist predators and thus may affect native species through predation. In previous studies, the food contents of bullfrogs were mostly examined at a single site. In the present study, the diet composition of post-metamorphic bullfrogs on eight islands (Daishan, Liuheng, Xiushan, Fodu, Taohua, Xiashi, Cezi, and Putuoshan) in the Zhoushan Archipelago, Zhejiang Province of China, were examined by using the stomach flushing method from June 30 to August 11 in 2005. A total of 391 individual frogs were measured, including 113 adults and 278 juveniles. The analysis of the stomach contents shows that, for adult bullfrogs, the most important prey (by diet volume) overall were Decapoda, Coleoptera, Odonata, Mesogastropoda, Raniformes, and Cypriniformes. For juvenile bullfrogs, these were Decapoda, Coleoptera, Cypriniformes, Odonata, Orthoptera, Hymenoptera, Lepidoptera larvae, Mesogastropoda, and Raniformes. Moreover, the prey size and diet volume increased with the body size of both adult and juvenile bullfrogs. The diet composition of primary preys of bullfrogs was significantly different among the islands. The results indicate that bullfrogs exert different predatory influences on native fauna at different sites and that bullfrogs are generalist predators with extensive ecological impacts on native fauna. __________ Translated from Biodiversity Science, 2006, 14 (5): 363–371 [译自: 生 物多样性]     

Fifteen years of climate change manipulations alter soil microbial communities in a subarctic heath ecosystem

Soil microbial biomass in arctic heaths has been shown to be largely unaffected by treatments simulating climate change with temperature, nutrient and light manipulations. Here, we demonstrate that more than 10 years is needed for development of significant responses, and that changes in microbial biomass are accompanied with strong alterations in microbial community composition. In contrast to slight or nonsignificant responses after 5, 6 and 10 treatment years, 15 years of inorganic NPK fertilizer addition to a subarctic heath had strong effects on the microbial community and, as observed for the first time, warming and shading also led to significant responses, often in opposite direction to the fertilization responses. The effects were clearer in the top 5 cm soil than at the 5–10 cm depth. Fertilization increased microbial biomass C and more than doubled microbial biomass P compared to the non-fertilized plots. However, it only increased microbial biomass N at the 5–10 cm depth. Fertilization increased fungal biomass and the relative abundance of phospholipid fatty acid (PLFA) markers of gram-positive bacteria. Warming and shading decreased the relative abundance of fungal PLFAs, and shading also altered the composition of the bacterial community. The long time lag in responses may be associated with indirect effects of the gradual changes in the plant biomass and community composition. The contrasting responses to warming and fertilization treatments show that results from fertilizer addition may not be similar to the effects of increased nutrient mineralization and availability following climatic warming.     

斑点嗜蓝孢孔菌化学成分、生物活性及水提物荧光猝灭研究

对斑点嗜蓝孢孔菌乙醇提取物进行分级萃取,利用柱层析技术得到6个单体化合物。经核磁数据比对为β-谷甾醇(1)、麦角甾醇(2)、麦角甾-7,22-二烯-3β-醇(3)、5,8-过氧麦角甾-6,22-二烯-3β-醇(4)、3-乙酰齐墩果酸(5)、白桦脂醇(6)。采用Alamar Blue法检测各有机相及单体化合物对NCI-H460人非小细胞肺癌细胞增殖的影响,用DPPH自由基清除法检测其抗氧化活性。利用荧光光谱及紫外-可见光光谱研究方法在模拟人体生理条件下,研究了斑点嗜蓝孢孔菌水提物与人纤维蛋白原的相互作用,实     

Temporal and spatial variability in nearshore bacterioplankton communities of Lake Michigan

The spatial and temporal variability of bacterial communities were determined for the nearshore waters of Lake Michigan, an oligotrophic freshwater inland sea. A freshwater estuary and nearshore sites were compared six times during 2006 using denaturing gradient gel electrophoresis (DGGE). Bacterial composition clustered by individual site and date rather than by depth. Seven 16S rRNA gene clone libraries were constructed, yielding 2717 bacterial sequences. Spatial variability was detected among the DGGE banding patterns and supported by clone library composition. The clone libraries from deep waters and the estuary environment revealed highest overall bacterial diversity. Betaproteobacteria sequence types were the most dominant taxa, comprising 40.2–67.7% of the clone libraries. BAL 47 was the most abundant freshwater cluster of Betaproteobacteria , indicating widespread distribution of this cluster in the nearshore waters of Lake Michigan. Incertae sedis 5 and Oxalobacteraceae sequence types were prevalent in each clone library, displaying more diversity than previously described in other freshwater environments. Among the Oxalobacteraceae sequences, a globally distributed freshwater cluster was determined. The nearshore waters of Lake Michigan are a dynamic environment that experience forces similar to the coastal ocean environment and share common bacterial diversity with other freshwater habitats.