Utility of DNA barcoding in native Oreochromis species

The importance of Oreochromis in worldwide aquaculture and regional fisheries motivates the study of their genetic diversity in their native range. In this article, all mitochondrial cytochrome c oxidase subunit I gene (COI) sequences of Oreochromis species are retrieved from Barcode of Life Data system to quantify the available DNA barcoding information from wild individuals collected within the native ranges of the respective species. It is found that 70% of the known species in the genus still lack a COI barcode, and only 15% of the available sequences are from within the respective native ranges. Many of the available sequences have been produced from specimens acquired from aquaculture and introduced, naturalized populations, making the assessment of variation within the original native range challenging. Analyses of the wild-collected fraction of available sequences indicated the presence of cryptic lineages within Nile tilapia Oreochromis niloticus and O. schwebischi, the occurrence of potential introgressive hybridization between O. niloticus and blue tilapia O. aureus, and potential ancestral polymorphism between Karonga tilapia O. karongae and black tilapia O. placidus. This article also reports a case of misidentification of O. mweruensis as longfin tilapia O. macrochir. These results stress the importance of improving the knowledge of genetic variation within the native ranges of Oreochromis species for better-informed conservation of these natural resources.     

Canopy throughfall links canopy epiphytes to terrestrial vegetation in pristine conifer forests

To what extent does epiphytic community composition in boreal forests reflect soil nutrient status? To answer this question, we investigated potential links between terrestrial plants and lichen-dominated communities in Picea glauca x engelmannii canopies in south-central British Columbia. We combined original data on vegetational composition in the ground and tree layers with published data on elemental uptake in standardized transplants of the lichen Lobaria pumonaria affixed to the lower branches of studied trees. Procrustean association metrics revealed a significant concordance between community composition among the epiphytic and terrestrial vegetation, which was stronger in Mn-enriched conifer canopy settings, and weaker within the cation-enriched dripzones of adjacent Populus trees. We also found that the NMDS1-gradient for each vegetation layer was strongly correlated with base cations (and inversely with Mn) in canopy throughfall, as well as with soil and bark pH. We conclude that elemental composition in canopy throughfall forms a functional link between terrestrial and epiphytic vegetation.     

格氏栲天然林林窗植物物种多样性与系统发育多样性

林窗环境异质性导致群落物种多样性与系统发育多样性(phylogenetic diversity, PD)存在差异, 研究不同大小的林窗中群落的物种多样性与系统发育多样性有助于揭示林下生物多样性的形成及维持机制。本文以格氏栲(Castanopsis kawakamii)天然林为研究对象, 通过Pearson相关性分析与广义线性模型探讨了林窗内物种多样性与系统发育多样性间的相互关系及其环境影响因素。结果表明: (1)大林窗(面积 > 200 m²)植物种类及多度均高于中林窗(50 m² ≤ 面积 < 100 m²)、小林窗(30 m² ≤ 面积 < 50 m²)和非林窗(面积 = 100 m²)。大林窗群落系统发育结构趋于发散, 中、小林窗和非林窗群落系统发育结构受到生境过滤和竞争排斥综合作用。(2)群落系统发育多样性指数与物种丰富度(species richness, SR)、Margalef丰富度指数和Shannon-Wiener指数均呈显著正相关, 这与林窗内稀有种种类组成多于优势种有关。(3)林窗面积对物种多样性存在显著正效应; 土壤全氮含量对系统发育多样性和系统发育结构存在显著正效应。林窗形成提高了格氏栲天然林群落物种多样性和系统发育多样性, 林窗面积与土壤全氮共同驱动了格氏栲天然林林窗物种多样性和系统发育多样性的变化。     

树冠结构对典型阔叶红松林生产力的影响

阔叶红松(Pinus koraiensis)林是东北东部山区的地带性森林植被, 阐明其生产力的影响因素, 对于理解温带森林生产力维持机制具有重要意义。该研究依托小兴安岭典型阔叶红松林9 hm²动态监测样地, 基于2005和2015年的30 m × 30 m样方内所有胸径>6.5 cm的木本植物的调查数据, 计算各样方的树冠结构复杂性、物种多样性和林分胸高断面积, 结合各样方的地形和土壤理化性质数据, 拟合结构方程模型, 定量分析影响典型阔叶红松林生产力的直接和间接因素。研究结果显示: 树冠结构复杂性和物种多样性与生产力显著正相关, 且树冠结构复杂性对生产力的影响显著高于物种多样性; 树冠结构复杂性对生产力的作用分为树冠垂直分层和树冠可塑性, 其中树冠垂直分层是树冠结构复杂性影响阔叶红松林生产力的主要因素, 而树冠可塑性无显著影响; 林分胸高断面积与生产力显著正相关, 其解释权重仅次于树冠结构复杂性, 树冠结构复杂性与物种多样性均通过影响林分胸高断面积对阔叶红松林生产力产生间接影响; 考虑不同树冠结构复杂性时, 坡度和土壤全磷含量代表的环境因素在调节生产力上发挥的作用存在差异, 移除树冠垂直分层的作用后两者与生产力呈显著的负相关关系。综上可知, 在典型阔叶红松林中, 树冠结构复杂性比物种多样性更有效地解释了生产力的变化, 同时不可忽视其他生物和非生物因素对生产力的作用。     

猫儿山铁杉相邻植株冠层机械磨损对枝叶性状的影响

机械磨损是邻体植物冠层接壤区域的重要生态过程之一, 对枝叶生理和形态特征具有重要影响。但是, 当前非常缺乏邻体植物冠层机械磨损对枝叶功能性状影响特征和权衡机制的深入研究。该研究以广西猫儿山的铁杉(Tsuga chinensis)为对象, 通过比较邻体冠层间机械磨损区优势枝、劣势枝与非机械磨损区的叶面积、叶长、叶宽、叶厚、比叶面积、叶干物质含量、叶干质量、末端枝含水率和枝直径的差异, 分析枝叶功能性状在机械磨损影响下的变异和权衡关系。结果显示: 机械磨损显著影响邻体冠层叶干物质含量、比叶面积和叶干质量。具体而言, 机械磨损区优势枝叶干物质含量显著大于劣势枝和非机械磨损区, 优势枝比叶面积显著低于劣势枝和非机械磨损区, 劣势枝叶干质量显著低于优势枝和非机械磨损区。其次, 机械磨损对枝叶性状关系的影响格局不同。叶面积-叶长在机械磨损区优势枝、劣势枝和非机械磨损区间表现出一致的正向关系; 叶面积-叶宽、叶面积-叶干质量、叶宽-叶厚、叶厚-末端枝直径和叶长-叶宽仅在机械磨损区优势枝显著正相关; 叶面积-末端枝直径和末端枝直径-末端枝含水率仅在劣势枝显著负相关; 叶干物质含量-叶厚仅在劣势枝显著正相关。其余性状关系在机械磨损区优势枝、劣势枝和非机械磨损区均不显著。以上结果表明, 森林植物邻体间的冠层机械磨损可显著改变枝叶功能性状的权衡关系。     

Understanding the key characteristics and challenges of pine barrens restoration: insights from a Delphi survey of forest land managers and researchers

Pine barrens are open‐canopy ecological communities once prevalent on sandy soils across the northern Great Lakes Region of the United States and Canada, though fire suppression and plantation forestry have now reduced them to a few isolated areas. Efforts to restore pine barrens are underway on some public lands, but lack of knowledge on the social and ecological issues and challenges that affect these projects impedes fuller progress. As a precursor to designing a public preference survey for pine barrens restoration, we sought input from those with expert knowledge about pine barrens. Using a three‐round modified Delphi survey, forest land managers and researchers identified the key characteristics of pine barrens and important current and future management challenges. Key characteristics were related to fire, landscape structure, plant and animal species, soils, and social themes. Current and future challenges were related to landscape, invasive species, social, economic, climate change, and science themes. Four social issues (education, fire acceptance, fire risk, aesthetics) were rated among the top current challenges but none of them maintained prominence as future challenges. Potential explanations for this shift are that the experts felt these social concerns would be resolved in time or that other issues, such as development pressures and budgets for carrying out restoration, would become greater future challenges. Our approach can be used by managers and researchers to better understand the ecosystems they seek to restore and to communicate with public stakeholders about restoration efforts.     

Restoration and Science: A Practitioner/Scientist's View from Rare Habitat Restoration at a Southern California Preserve

Researchers reexamining the relationship between restoration science and practice report a continuing scientist‐practitioner gap. As a land manager with scientific training, I offer my perspective of the chasm and describe a restoration practice infused with as much science as the realities of limited budget and time allow. The coastal sage scrub (CSS) restoration project at Starr Ranch, a 1,585 ha Audubon preserve in southern California, combines non‐chemical invasive species control, restoration, and applied research. Our practices evolve from modified scientific approaches and the scientific literature. Results from experiments with non‐optimum replication (on effects of seed rates, soil tamping, and timing of planting) nonetheless had value for management decisions. A critical practice came from academic research that encouraged cost‐effective passive restoration. Our passive restoration monitoring data showed 28–100% total native cover after 3–5 years. Another published study found that restoration success in semiarid regions is dependent on rainfall, a finding vital for understanding active restoration monitoring results that showed a range of 0–88% total native cover at the end of the first season. Work progresses through a combination of applied research, a watchful eye on the scientific literature, and “ecological intuition” informed by the scientific literature and our own findings. I suggest that it is less critical for academic scientists to address the basic questions on technique that are helpful to land managers but rather advocate practitioner training in methods to test alternative strategies and long‐term monitoring.     

微生物全基因组测序组装中的g印填补方法

目的：研究和开发高通量测序全基因组组装过程中的填补gap的方法。方法：研究组装软件的算法,使用Perl语言编写自动填补gap的程序,并建立全基因组组装的流程。结果：提出了填补gap的末端延伸法,并使用Perl语言进行了编程;在对立克次体高通量测序的组装过程中,这些方法能大大减少gap的数量。结论：本研究提出的末端延伸法能够高效填补全序列组装过程中出现的gap,具有很强的实用性。     

The biomechanical effect of the collar of a femoral stem on total hip arthroplasty

To investigate the biomechanical effect of collars, finite element analyses are carried out through two hip joints that are implanted using collared and collarless stems, respectively, and an intact hip joint model. For the analyses, the sacrum, coxal bone, and the cancellous and cortical bones of a femur are modelled using finite elements based on X-ray computed tomographic images taken from a 27-year-old woman. From the results, it is found that a collar with perfect calcar contact prevents stem subsidence and decreases the proximal–lateral gap and the lateral stem tilting. Therefore, it can impart reasonable biomechanical stability for total hip arthroplasty. However, its low load transmission ability and increased stem tilting effect due to the imperfect contact between the collar and the calcar are found to be serious problems that need to be solved. Results of clinical follow-up are presented for supporting the computational results.