Growth dynamics and biomass allocation of Eleocharis sphacelata at different water depths: observations, modeling, and applications

Imbalanced biomass allocation patterns in emergent aquatic plants to above and below-ground structures as a response to climatic variations and water depth were investigated on the basis of observation of three stable homogeneous populations established under different water regimes and climatic environments in Goulburn and Ourimbah, New South Wales, Australia, from August 2003 to December 2004. The growth of shoots depended on water inundation-drawdown patterns and climatic variations. Shoot density was greater in shallow water but with shorter shoot length and less maximum above-ground biomass density than for plant stands in deep water. Deep-water populations attained higher below-ground biomass with higher above to below-ground biomass ratio than for the shallow-water population. Translocation of carbohydrate reserves between above and below-ground organs in deep-water populations were mostly downward throughout the year whereas the depletion–recharge pattern varied seasonally in shallow water populations. Shoots of deep-water populations grew year-round whereas in shallow water shoots died off after recession of the water level with no re-growth afterward, showing that Eleocharis sphacelata is better adapted to deep water and is stressed under shallow-water conditions. A mathematical model was formulated to describe the growth patterns of E. sphacelata and subsequently to predict the effect of water depth on production. Model simulations are in satisfactory agreement with observed patterns of growth. The model also predicts that maximum production decreases sharply with increasing water depth.     

光动力疗法辅助治疗轻中度牙周炎的疗效观察

目的:探讨光动力疗法(PDT)辅助治疗轻中度牙周炎患者的临床疗效。方法:选取我院2016年1月-2017年8月收治的轻中度牙周炎患者46例为研究对象,共选取患牙276颗,随机分为观察组与对照组,每组138颗患牙,对照组予以龈下刮治术和根面平整术(SRP)治疗,观察组在对照组的基础上联合PDT治疗,比较治疗前、治疗后1个月、2个月、3个月观察两组患者的牙周袋探诊深度(PD)、探诊出血(BOP)阳性率、出血指数(BI)。结果:治疗后1个月、2个月、3个月,两组PD均随着时间的推移逐渐变浅(P0.05),且观察组治疗后各时间点均浅于对照组(P0.05);两组BOP阳性率均较治疗前降低,且观察组治疗后各时间均低于对照组(P0.05);两组BI随着时间的推移呈逐渐下降趋势(P0.05),且观察组治疗后各时间点BI均低于对照组(P0.05)。结论:PDT辅助治疗轻中度牙周炎患者的临床疗效较好,其能减小PD,降低BI和BOP阳性率。     

An evaluation of sequencing coverage and genotyping strategies to assess neutral and adaptive diversity

Whole genome sequences (WGS) greatly increase our ability to precisely infer population genetic parameters, demographic processes, and selection signatures. However, WGS may still be not affordable for a representative number of individuals/populations. In this context, our goal was to assess the efficiency of several SNP genotyping strategies by testing their ability to accurately estimate parameters describing neutral diversity and to detect signatures of selection. We analysed 110 WGS at 12× coverage for four different species, i.e., sheep, goats and their wild counterparts. From these data we generated 946 data sets corresponding to random panels of 1K to 5M variants, commercial SNP chips and exome capture, for sample sizes of five to 48 individuals. We also extracted low‐coverage genome resequencing of 1×, 2× and 5× by randomly subsampling reads from the 12× resequencing data. Globally, 5K to 10K random variants were enough for an accurate estimation of genome diversity. Conversely, commercial panels and exome capture displayed strong ascertainment biases. Besides the characterization of neutral diversity, the detection of the signature of selection and the accurate estimation of linkage disequilibrium (LD) required high‐density panels of at least 1M variants. Finally, genotype likelihoods increased the quality of variant calling from low coverage resequencing but proportions of incorrect genotypes remained substantial, especially for heterozygote sites. Whole genome resequencing coverage of at least 5× appeared to be necessary for accurate assessment of genomic variations. These results have implications for studies seeking to deploy low‐density SNP collections or genome scans across genetically diverse populations/species showing similar genetic characteristics and patterns of LD decay for a wide variety of purposes.     

Phylogenomics using low‐depth whole genome sequencing: A case study with the olive tribe

Species trees have traditionally been inferred from a few selected markers, and genome‐wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference‐based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide‐distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome‐wide phylogenetic trees can be inferred from low‐depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large‐scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.     

Roadside verges and cemeteries: Comparative analysis of anthropogenic orchid habitats in the Eastern Mediterranean

Several important habitats have become threatened in the last few centuries in the Mediterranean Basin due to major changes adopted in land‐use practices. The consequent loss of natural and seminatural orchid habitats leads to the appreciation of small anthropogenic habitats, such as cemeteries and roadside verges. Colonization of cemeteries and roadside verges by orchids has long been known, but no study to date compared the suitability of these two anthropogenic habitats for orchids. Therefore, in this paper our aim was to survey cemeteries and roadside verges and to compare these two habitats regarding their role in conserving Mediterranean terrestrial orchids. We conducted field surveys in three Mediterranean islands, Cyprus, Crete, and Lesbos, where both cemeteries and roadside verges were sampled on a geographically representative scale. We found a total of almost 7,000 orchid individuals, belonging to 77 species in the two anthropogenic habitat types. Roadside verges hosted significantly more individuals than cemeteries in Crete and Lesbos, and significantly more species across all three islands. Our results suggest that although cemeteries have a great potential conservation value in other parts of the world, intensive maintenance practices that characterized cemeteries in these three islands renders them unable to sustain valuable plant communities. On the other hand, roadside verges play a prominent role in the conservation of Mediterranean orchids in Cyprus and Greece. The pioneer status of roadside verges facilitates their fast colonization, while roads serve as ecological corridors in fragmented landscapes.     

干旱半干旱区地下水埋深对沙地植物土壤系统演变的驱动作用综述

在干旱半干旱生态脆弱区,地下水是限制植物种类组成、数量和生长发育的关键因素之一。近年来由于气候变化与土地利用强度的增加,我国北方普遍出现以极端气候变化、地表水体萎缩和地下水位下降为特征的生态过程,对区域生态系统安全和可持续发展构成严重威胁。而有关干旱半干旱区地下水埋深变化驱动退化植被恢复和稳定性维持方面的系统研究尚存不足。系统总结了地下水埋深变化分别对植物、土壤产生的影响及其三者间相互作用关系,比较分析了前人的研究成果,归纳总结了地下水埋深变化的驱动作用和影响因素,以及干旱半干旱区地下水埋深变化对植物土壤系统影响的预测模型研究,以期为今后应对地下水埋深变化制定生态保护策略提供理论指导依据。对本研究做了展望。     

Plant–soil feedback during biological invasions: effect of litter decomposition from an invasive plant (Sphagneticola trilobata) on its native congener (S. calendulacea)

生物入侵过程中的植物-土壤反馈：一种入侵植物的凋落物分解对其本地近缘植物的影响 植物入侵可通过正或负的植物-土壤反馈效应改变土壤的生物和非生物性质,从而影响入侵栖息地的土壤理化性质。许多入侵物种的凋落物分解可增加土壤养分,降低本地植物多样性,并导致进一步的植物入侵。关于入侵植物凋落物在不同土壤类型及深度分解及反馈效应的研究依然很少。本研究旨在明确入侵植物南美蟛蜞菊(Sphagneticola trilobata)凋落物在不同土壤类型和不同土壤深度条件下的分解情 况及其对本地近缘植物蟛蜞菊(S. calendulacea)生理生长的影响。将装有南美蟛蜞菊凋落物的尼龙袋加入到不同深度(即0、2、4 和6 cm)的砂土、营养土和粘土中,经6个月的分解后,回收凋落物袋并计算分解速率,随后在凋落物分解处理后的土壤中种植本地蟛蜞菊,并在生长期结束时测量其生理生态指标。研究结果表明,所有处理土壤类型中,凋落物在土壤深度为2和4 cm处分解后显著增加了土壤养分,而对本 地蟛蜞菊的叶片叶绿素、叶氮含量等生长指标表现为负效应。因此,入侵植物南美蟛蜞菊凋落物分解对土壤养分表现为正的反馈效应,而对本地植物蟛蜞菊的生长表现为负效应。我们的研究结果还表明,入侵植物的凋落物分解对土壤和本地物种的影响还因凋落物分解所在的土壤深度而显著不同。未来的研究应侧重于入侵栖息地中更多本地和入侵物种的植物-土壤反馈效应,以及更多土壤类型和土壤深度的入侵植物凋落物效应。     

Influence of latitude, water depth, day v. night and wet v. dry periods on the species composition of reef fish communities in tropical Western Australia

Trap sampling over reefs in deep (mean = 20 m) and shallow (mean = 10 m) waters along c. 1500 km of coastline in tropical north‐western Australia during both day and night and in wet and dry periods yielded 23 377 fishes, representing 32 families, 58 genera and 119 species. Individuals of the Serranidae, Lutjanidae, Lethrinidae and Carangidae contributed 88·9% to the total catch. The ichthyofaunal compositions of the Kimberley, Canning and Pilbara bioregions were relatively discrete. Species composition was influenced far more by location (latitude) than by water depth, period and time of day, and underwent a gradational change southwards. The latter change reflected differences in the trends exhibited by the relative abundances of certain species with increasing latitude and the confinement of other species largely to particular regions. The three most abundant species, i.e. Lethrinus sp. 3, Lutjanus carponotatus and Lethrinus laticaudis contributed 34·8, 20·8 and 11·6% to the total catch, respectively. The first species was rarely recorded in the two most northern locations and was abundant in the four most southern locations, whereas the last two species were relatively more abundant in northern than in southern locations. Lutjanus bitaeniatus and Lutjanus johnii were found exclusively at the two locations in the Kimberley region, whereas Abalistes stellatus, Pentapodus emeryii and Lethrinus nebulosus were not caught in this region but were found in both locations of the Canning and Pilbara regions. The species composition in deep and shallow waters at each location almost invariably differed significantly between day and night and between dry and wet periods, with species such as L. bitaeniatus, L. johnii, Lutjanus sebae and A. stellatus being more abundant over deep reefs, whereas L. carponotatus, L. laticaudis, Siganus fuscescens and Lethrinus lentjan were more numerous over shallow reefs. Species such as L. johnii and Lethrinus atkinsoni were relatively more important in night‐time than daytime catches, whereas the reverse applied to Lethrinus lentjan, L. laticaudis and Choerodon cyanodus. Lethrinus sp. 3 and L. laticaudis were relatively more important in catches during the dry than wet period.