Manta Matcher: automated photographic identification of manta rays using keypoint features

For species which bear unique markings, such as natural spot patterning, field work has become increasingly more reliant on visual identification to recognize and catalog particular specimens or to monitor individuals within populations. While many species of interest exhibit characteristic markings that in principle allow individuals to be identified from photographs, scientists are often faced with the task of matching observations against databases of hundreds or thousands of images. We present a novel technique for automated identification of manta rays (Manta alfredi and Manta birostris) by means of a pattern‐matching algorithm applied to images of their ventral surface area. Automated visual identification has recently been developed for several species. However, such methods are typically limited to animals that can be photographed above water, or whose markings exhibit high contrast and appear in regular constellations. While manta rays bear natural patterning across their ventral surface, these patterns vary greatly in their size, shape, contrast, and spatial distribution. Our method is the first to have proven successful at achieving high matching accuracies on a large corpus of manta ray images taken under challenging underwater conditions. Our method is based on automated extraction and matching of keypoint features using the Scale‐Invariant Feature Transform (SIFT) algorithm. In order to cope with the considerable variation in quality of underwater photographs, we also incorporate preprocessing and image enhancement steps. Furthermore, we use a novel pattern‐matching approach that results in better accuracy than the standard SIFT approach and other alternative methods. We present quantitative evaluation results on a data set of 720 images of manta rays taken under widely different conditions. We describe a novel automated pattern representation and matching method that can be used to identify individual manta rays from photographs. The method has been incorporated into a website (mantamatcher.org) which will serve as a global resource for ecological and conservation research. It will allow researchers to manage and track sightings data to establish important life‐history parameters as well as determine other ecological data such as abundance, range, movement patterns, and structure of manta ray populations across the world.     

Making small molecules in plants: A chassis for synthetic biology-based production of plant natural products

Plant natural products have been extensively exploited in food,medicine,flavor,cosmetic,renewable fuel,and other industrial sectors.Synthetic biology has recently emerged as a promising means for the cost-effective and sustainable production of natural products.Compared with engineering microbes for the production of plant natural products,the potential of plants as chassis for producing these compounds is underestimated,largely due to challenges encountered in engineering plants.Knowledge in pl...     

芳香类天然产物的合成生物学研究进展

植物芳香类天然产物具有重要的药用价值,可制成具有抗菌、抗炎、镇痛、抗氧化、杀虫驱虫、祛痰止咳、安神镇静和抗肿瘤等药效的医药保健用品.然而,由于植物中芳香类天然产物含量较低并且难以提取和纯化,严重限制了其工业化生产及应用.合成生物学和代谢工程技术的发展为天然产物的生产提供了新的思路,可以利用人工微生物细胞工厂来实现多种芳...     

A streamlined, bi-organelle, multiplex PCR approach to species identification: Application to global conservation and trade monitoring of the great white shark, Carcharodon carcharias

The great white shark, Carcharodoncarcharias, is the most widely protectedelasmobranch in the world, and is classified asVulnerable by the IUCN and listed on AppendixIII of CITES. Monitoring of trade in whiteshark products and enforcement of harvest andtrade prohibitions is problematic, however, inlarge part due to difficulties in identifyingmarketed shark parts (e.g., dried fins, meatand processed carcasses) to species level. Toaddress these conservation and managementproblems, we have developed a rapid, moleculardiagnostic assay based on species-specific PCRprimer design for accurate identification ofwhite shark body parts, including dried fins. The assay is novel in several respects: Itemploys a multiplex PCR assay utilizing bothnuclear (ribosomal internal transcribed spacer2) and mitochondrial (cytochrome b) locisimultaneously to achieve a highly robustmeasure of diagnostic accuracy; it is verysensitive, detecting the presence of whiteshark DNA in a mixture of genomic DNAs from upto ten different commercially fished sharkspecies pooled together in a single PCR tube;and it successfully identifies white shark DNAfrom globally distributed animals. Inaddition to its utility for white shark trademonitoring and conservation applications, thishighly streamlined, bi-organelle, multiplex PCRassay may prove useful as a general model forthe design of genetic assays aimed at detectingbody parts from other protected and threatenedspecies.     

基于保护地役权的自然保护地适应性管理方法探讨: 以钱江源国家公园体制试点区为例

我国的自然保护地普遍存在着科学管控难、统一管理难和资金供给难等问题, 即便是国家公园体制试点区也不例外。本文以钱江源国家公园体制试点区为例, 设计了基于细化保护需求的保护地役权制度, 以探索一种能解决上述问题并能体现生态补偿的适应性管理方法, 包括: 细化主要保护对象的管理需求, 结合土地利用类型, 确定实施保护地役权的空间范围; 辨析保护需求和原住民生产、生活之间的关系, 形成正负行为的准则并以行为清单的形式体现; 从生态系统监测指标改善情况、正负行为遵守情况和社区能力建设三个维度制定地役权制度的评价方法; 据此形成地役权合同, 明确供役地人和需役地人的权责利, 形成考虑保护绩效的生态补偿方案。这种方法可以解决自然保护地因为权属不一致造成的生态系统和景观破碎化问题, 缓解社区发展和生态保护之间的矛盾, 在我国南方集体林地占比较高的自然保护地具有适用性。     

A teaching exercise for the identification of bacteria using an interactive computer program

An interactive computer program written in Fortran is described which provides an exercise in the identification of bacteria. The program, IDEN, provides a novel way of enhancing a student's approach to systematic bacteriology and numerical identification procedures. An unknown bacterium is assigned to a student who is provided with a list of possible species and a list of tests which may be carried out. The student's objective is the correct identification of the unknown in the most economical manner. An indication is given concerning the way in which this program can be used to enhance theoretical instruction and practical investigation.     

自然保护地整合优化的景观格局变化分析——以贵州省思南县为例

自然保护地整合优化是我国重构自然保护地体系、衔接三条控制线划定、完善国土空间规划的重要举措。利用自然保护地整合优化成果、国土三调数据,综合运用GIS空间分析、景观格局指数和保护地边界分析法,对贵州思南县自然保护地整合优化各阶段景观格局的变化特征及其合理性进行了分析。结果表明：（1）整合优化后土地利用/覆盖组成变化显著,耕地、建设用地显著减少,优势景观林地面积增加。（2）整合优化后,思南县自然保护地景观异质性降低、优势度增强、破碎度增加。（3）各斑块类型的复杂性和异质性降低,林地优势度增强,但耕地、园地的破碎度增加,整合优化未造成优势景观的破碎化。（4）整合优化后,自然保护地边界复杂度显著提高,自然保护区、地质公园变化最明显,将给自然保护地勘界定桩增加难度。（5）耕地、建设用地、林地变化是思南县自然保护地景观格局变化的主要因素,耕地、建设用地主要作为矛盾调出自然保护地,而林地则主要作为破碎化斑块伴随矛盾一并调出。本研究自然保护地整合优化方案围绕矛盾和问题开展调整,所反映的景观格局变化,与整合优化调整规则限定的内容相适应,整合优化方案总体可行、合理。由于存在的破碎化、边界复杂化、区域分离等问题,在整合优化过程中应进一步优化调整规则,统一数据精度,尽量避免此类问题的产生。景观格局指数变化所反馈的信息可为自然保护地整合优化的科学开展及其成果的合理性评价提供一定参考,引入成果评估机制对自然保护地整合优化工作具有重要意义。     

Flank spot number and its significance for systematics,taxonomy and conservation of the near‐threatened Mediterranean trout Salmo cettii: evidence from a genetically pure population

The number of spots on the flank of the Mediterranean trout Salmo cettii population from Tellesimo Stream in Sicily, Italy, varied between seven and 37, with a median and mode of 21, numbers much lower than those reported in the literature and different from those of other Italian trout populations. This finding could be ascribed to the phenotypic plasticity of the species or, alternatively, could provide evidence to support the different origin of Sicilian autochthonous trout. Given the ease of use of this character for the identification of native fish, it could be particularly important for conservation and management purposes.     

基于动物适宜栖息地的北京市自然保护地保护成效评估

栖息地是野生动物赖以生存的基础,明晰物种的适宜栖息地分布是切实加强野生动物保护、提高生物多样性保护成效的重要基础。北京市野生动植物资源丰富,也建立了一系列自然保护地以加强对野生动物的保护。当前亟需系统评估北京市现有自然保护地体系对野生动物适宜栖息地的保护成效,为未来北京市野生动物保护管理和自然保护地体系整合工作优化提供科学指导。研究选取了北京地区6个较为典型的野生动物为主要研究对象,包括黑鹳(Ciconia nigra)、褐马鸡(Crossoption mantchuricum)、大鸨(Otis tarda)、鸳鸯(Aix galericulata)、金雕(Aquila chrysaetos)和斑羚(Naemorhedus griseus),利用MaxEnt模型和ArcGIS的空间分析功能分析其适宜栖息地的分布;将自然保护地与适宜栖息地相叠加,识别其适宜栖息地的分布热点和保护空缺,进而评估了北京市现有自然保护地体系的保护成效。研究结果表明,6个研究物种在现有的自然保护地体系中均得到了不同程度的保护,其中褐马鸡的受保护率最高(92.82%),鸳鸯的受保护率最低(13.66%)。各类自然保...     

Using Head Patch Pattern as a Reliable Biometric Character for Noninvasive Individual Recognition of an Endangered Pitviper Protobothrops mangshanensis

Mangshan pitviper, Protobothrops mangshanensis(formerly Zhaoermia mangshanensis) is endemic to China. Unfortunately, due to the decreasing size of its wild populations, this snake has been listed as critically endangered. Research carried out on the Mangshan pitviper's population ecology and captive reproduction has revealed that the unique head patch patterns of different individuals may potentially be used as a noninvasive recognition biometric character. We collected head patch pattern images of 40 individuals of P. mangshanensis between 1994 and 2011. By comparing each pitviper's head patch pattern, we found that the head patch pattern of individual snakes was different and unique. Additionally, we observed and recorded the head patch pattern characters of four adults and five juveniles before and after ecdysis. Our findings confirmed that head patch patterns of Mangshan pitvipers are unique and stable, remaining unchanged after ecdysis. Thus, individuals can be quickly identified by examining the head patch pattern within a specific recognition area on the head. This method may be useful for noninvasive individual recognition in many other species that display color patch pattern variations, especially in studies of endangered species where the use of invasive marking techniques is undesirable.     

Genetic and reproductive evidence for two species of ornate wobbegong shark Orectolobus spp. on the Australian east coast

This study reports on evidence for reproductive isolation among Orectolobus ornatus and Orectolobus halei, two previously cryptic and recently redescribed species of wobbegong shark (Orectolobiformes: Orectolobidae) from the east coast of Australia. The evidence is based on disparity in size at sexual maturity, diagnostic nuclear and mitochondrial DNA variants, and marked phylogenetic divergence. Plots of total length (L_T) and maturity for the two species were non‐overlapping and illustrative of statistically significant size dimorphism. Genetic analyses and phylogenetic reconstruction did not provide indication of hybridization between O. ornatus and O. halei. In fact, sequence divergence between them was higher than in comparisons with another congeneric and largely co‐distributed wobbegong species (Orectolobus maculatus). The assumption of a molecular clock revealed that the two species have evolved in isolation for c. 3·9 million years. These results challenge a paradigm often mentioned in the biodiversity literature that most cryptic species are the product of recent speciation events and will contribute to the development of effective management strategies for wobbegong sharks.     

Effects of ground cover (straw and compost) on the abundance of natural enemies and soil macro invertebrates in vineyards

1 Herbicides are commonly applied under grapevines in Australia to remove weeds and thereby to avoid water loss through transpiration. 2 Interest in sustainability promotes a reduction in chemical inputs, including herbicides, leading to trials with surface mulches to suppress weeds. 3 Surface mulches may also influence the abundance of a range of invertebrates. Potentially, an increase in natural enemies will contribute to pest control and encourage a reduction in pesticide application. 4 We used three trapping methods and direct soil sampling to assess invertebrates at ground level, in the canopy and in the soil to determine the influence of mulch on natural enemies, potential pests and soil macroinvertebrates, including earthworms. 5 Collections sorted to family demonstrated that the addition of straw or compost mulches increased natural enemies collected with pitfall traps and soil organisms. However, there was no clear indication of the overall superiority of either mulch. 6 Abundance of ground beetles, parasitoid Hymenoptera and spiders collected with pitfall traps were increased by the addition of mulches. In the canopy, predatory and parasitic Diptera and predatory Hemiptera increased after mulching. 7 Earthworms collected by hand sorting soil increased with straw mulching. 8 No influence on pests was detected. Although Lepidoptera and Sigmurethra, collected in pitfall traps, increased with straw mulching, neither included pest species. 9 The results are discussed with reference to the potential economic impact of mulches.     

野生绿孔雀生态学及保护生物学研究进展

绿孔雀(Pavo muticus)是我国国家I级重点保护野生动物, 也是中国传统文化中具有重要代表意义的物种。在历史上, 绿孔雀曾广泛分布于我国南部大部分地区, 但目前在国内只分布于云南省部分地区。在国外有绿孔雀分布的东南亚国家, 绿孔雀同样经历了从广布到局部甚至零星分布的严重退缩。关于野生绿孔雀生态学和种群现状的研究已开展了不少工作, 但仍有许多空缺; 而该物种面临的生存威胁给保护和管理工作带来了巨大挑战。本文通过梳理国内外野生绿孔雀生态学和保护生物学方面的研究, 阐述了绿孔雀在国内外种群和分布区的变迁与现状、栖息地选择、与同域分布物种的种间关系, 分析了主要的致危因素, 同时为今后的研究方向和保护措施提出了建议。现有研究显示: (1)绿孔雀在国内的种群数量已不足500只, 在东南亚主要分布于中南半岛的部分区域及印度尼西亚的爪哇岛; (2)绿孔雀对水源地有很强的依赖, 倾向于利用远离居民点的区域, 并偏爱利用生境开阔、旱季落叶的热带季雨林, 喜爱与大型有蹄类混群; (3)大型猫科动物可能是绿孔雀潜在的天敌; (4)偷猎和栖息地丧失是绿孔雀面临的最主要的致危因素。综上, 我们建议尽快建立起中国绿孔雀监测网络, 评估野生绿孔雀的种群动态, 识别不同区域绿孔雀的受胁因素, 并结合分子生物学等技术开展保护遗传学研究。在保护实践上, 应在目前中国野生绿孔雀分布较为集中、原生栖息地保存较为完整的红河(元江)中上游河谷地带建立自然保护区, 同时加强巡护工作, 启动栖息地恢复工程, 并杜绝在野生绿孔雀栖息地附近的蓝孔雀(Pavo cristatus)养殖。     

中国保护区分类的研究

保护区是一个泛称,由于其建立的目的、要求和本身所具备的条件不同,所以具有多种多样的类型,不同类型管理的侧重点也有所区别.以保护区管理的目标为原则划分第一级分类单位,共有5个类型,即:严格的保护区、国家公园、保护景观、栖息地/物种管理区、资源管理保护区.再以保护对象原则划分第二、三级分类单位,共同构成一个完整的分类系统,以适应保护区事业日益发展的要求.     

Not just for the birds: Spiders as natural enemies of spruce budworm (Choristoneura fumiferana,Clem.)

(1) The eastern spruce budworm (Choristoneura fumiferana, Clem.) is a native irruptive forest pest that defoliates spruce-fir forests throughout North America's boreal zone. (2) Past studies suggest that successful spruce budworm population control requires high natural mortality from a variety of sources, including predators, especially from parasitoids and birds. While well represented in many different ecosystems, the role of generalist predatory spiders in these boreal systems remains largely unstudied. (3) To determine the identity and percentage of spiders preying upon spruce budworm, we hand-collected spiders from balsam fir (Abies balsamea) in stands with relatively high spruce budworm densities from forests in insular Newfoundland and Labrador, Canada. (4) Using a spruce budworm-specific TaqMan real-time PCR assay, we successfully amplified spruce budworm DNA in 32% of collected spiders. After spider molecular barcoding, we found the web builders Grammonota angusta Dondale, Pityohyphantes (aff. subarcticus), Dictyna brevitarsa Emerton and Estrandia grandaeva (Keyserling) represented 58% of the spiders feeding on spruce budworm, and the wandering hunter Philodromus rufus Dondale represented 11.8%. (5) Our molecular approach was an effective means with which to identify recently consumed prey and natural enemies in this boreal system.     

A poor imitation of a natural process: A call to reconsider the iPSC engineering technique

Reprogramming somatic cells into a pluripotent state is expected to initiate a new era in medicine. Because the precise underlying mechanism of reprogramming remains unclear, many efforts have been made to optimize induced pluripotent stem cell (iPSC) engineering. However, satisfactory results have not yet been attained. In this review, we focus on recent roadblocks in iPSC reprogramming engineering, such as the inefficiency of the process, tumorigenicity and heterogeneity of the generation. We conclude that cell reprogramming is a naturally occurring phenomenon rather than a biological technique. We will only be able to mimic the natural process of reprogramming when we fully understand its underlying mechanism. Finally, we highlight the alternative method of direct conversion, which avoids the use of iPSCs to generate cell materials for patient-specific cell therapy.