一种鱼类DNA的非损伤检测方法

为了减少和改变对濒危野生鱼类的大量伤害性取样,本文探索了从非损伤性取样的鱼类体表粘液样品中提取鱼类基因组DNA的方法,并用常用的两种分子标记(Cyt b和D-Loop)检测了分离到的粘液DNA。结果表明,从非损伤性取样的鱼类粘液样品中能够分离到高质量的鱼类基因组DNA,可用于后续的研究工作。鱼类体表粘液的非损伤性取样及其DNA提取,为濒危野生鱼类遗传学研究提供了一种新的非损伤性DNA检测技术。     

非损伤性取样法在保护遗传学研究中的应用

通过对非损伤怀取样法的种类以及毛发的非损伤性取样分析方法、口腔脱落细胞的非损伤性取样分析方法、馆藏标本的非损伤性取样分析方法、粪便的非损伤性取样分析方法和其它样品的非损伤性取样分析方法的介绍,就非损伤取样法在保护遗传学中的应用及其优点、局限性和应用前景作了介绍、分析和讨论。     

应用非伤害性取样提取番鸭毛囊组织总RNA

目的:寻求一种从番鸭毛囊组织中高效提取总RNA的方法。方法:探讨了伤害性取样(剪切皮肤毛囊)、非伤害性取样(直接拔取毛囊)2种不同毛囊取样法对总RNA提取质量的影响,并对常用RNA提取方法TRIzol法中研磨和组织匀浆步骤细节稍加改进,琼脂糖电泳检测总RNA质量。结果:2种毛囊取样方法均能提取出高质量的总RNA,其28S、18S和5S条带清晰可见,无DNA污染。结论:非伤害性取样法可作为番鸭毛囊组织总RNA提取的适用取样方法。     

非损伤性取样研究进展

非损伤性取样即在不捕获、触及,甚至是未亲眼见到动物的情况下,收集不同形式的样品获取样品中的DNA。通过介绍各种类型非损伤性取样的研究进展,就该取样存在的问题及现有解决方法进行讨论,并在此基础上对非损伤性取样的研究和应用前景进行了分析,以期对进一步研究提供有价值的参考。     

黑麂粪便DNA提取及其PCR检测

采集了黑麂(Muntiacus crinifrons)的新鲜粪便以及在野外自然条件下保存较长时间的粪便样品,晾干后带回实验室,提取其DNA;同时提取黑麂肌肉、皮张样品的DNA,用以对比粪便样品的提取效果。电泳检测结果显示,此方法使用实验室中常用的分子生物学试剂,可以从黑麂粪便样品中抽提到高质量的粪便DNA并克服分子粪便学研究中常见的PCR反应抑制物的影响。为其它濒危鹿科动物的非损伤性取样提供了的新途径,为其遗传结构、遗传多样性现状等研究提供了更加广阔的取材空间。     

非损伤性取样样品中富集宿主DNA的研究进展

非损伤性取样被广泛应用在动物保护遗传学、分子生态学和分子进化等研究领域.随着基因组测序技术的发展和基因组学时代的到来,如何从非损伤性取样样品中获取能够用于进行基因组测序的高质量DNA是研究者面临的难题.本文总结和比较了非损伤性取样中最常用的粪便样品和考古材料或博物馆标本两类样品中富集宿主DNA的方法及应用,以期为非损伤...     

体表擦拭取样在两栖动物保护遗传学研究中的应用

相比于其他取样方法,非损伤性取样对动物的伤害可以降到最低,因而在动物保护研究中有着重要的价值。在两栖类中通过体表擦拭进行非损伤性取样的方法已有报道,但是相关研究仅局限于零星物种,且均是在实验室环境下完成取样,并不适用于野外就地取样。本研究对四川申果庄省级大熊猫自然保护区内有尾两栖类及无尾两栖类6科10属11种进行了就地擦拭取样。线粒体基因序列分析表明,体表擦拭取样法获得的DNA能满足常规的分子生物学实验要求,可用于水生、陆栖等各种两栖动物类群,可在两栖类保护遗传学研究中广泛应用。     

对影响哺乳动物粪便DNA提取相关因素的探讨

从动物粪便中提取DNA是一种优秀的非损伤性取样方法,然而在实际操作中成功提取高质量粪便DNA却是一件不太容易的事情.粪便DNA的获取不仅与提取方法有关,还受到样品采集、保存、二次取样、预处理等相关环节的影响,对其中任一环节的忽视都会导致试验达不到理想效果.综合国内外具有代表性的哺乳动物粪便DNA提取技术,对有关环节进行了详细的评述,并对PCR扩增中的常见问题进行了分析和讨论.     

基于分子宏条形码分析四川卧龙国家级自然保护区雪豹的食性

作为中亚和青藏高原山地生态系统中的顶级捕食者, 雪豹(Panthera uncia)对于维持食物网结构和生态系统稳定性有重要作用。了解雪豹的食性组成和变化对于理解其生态系统功能和物种间相互作用有重要意义。以往的雪豹食性分析多基于对其粪便中食物残渣的形态学鉴定, 但准确度受人员经验和主观因素影响较大。邛崃山脉位于雪豹分布区东南缘, 该区域的雪豹种群规模小且相对孤立, 研究匮乏。本研究基于非损伤性取样, 在邛崃山脉的卧龙国家级保护区采集疑似雪豹粪便样品38份, 首先提取粪便DNA, 并扩增线粒体DNA 16S rRNA基因片段进行分子物种鉴定, 确定其中22份为雪豹粪便样品。随后, 利用脊椎动物通用引物和雪豹特异性阻抑引物扩增粪便DNA中的食物成分, 并进行高通量测序, 分析雪豹食性构成。食性分析结果显示岩羊(Pseudois nayaur)是卧龙地区雪豹最主要的食物, 在67%的样品中均有检出。家牦牛(Bos grunniens)在33%的样品中出现, 也在雪豹食性中占较高比例。此外, 鼠兔(Ochotona spp.)和鸟类也在少量样品中发现。可见, 野生猎物是卧龙地区雪豹的主要食物资源; 与大世界大多数其他地区的雪豹食性相同, 野生大型有蹄类是雪豹最重要的食物。然而家畜(牦牛)在卧龙雪豹食谱中有相当高的占比, 显示该区域内可能存在较为严重的由雪豹捕食散养家畜引起的人兽冲突问题。     

一种从鸟类剥制标本提取DNA的改进方法

应用非损伤性取样的方法,收集鸟类剥制标本的皮肤组织和羽毛,用无水乙醇、浸泡液预处理的方法抽提DNA,结果两者都可提取DNA供PCR扩增。将PCR产物经序列测定和比对分析,证明提取的DNA为目的DNA,表明本试验方法可行。鸟类剥制标本的皮肤组织和羽毛可以作为研究种群遗传学的资源。     

Magic bullets and golden rules: data sampling in molecular phylogenetics

Data collection for molecular phylogenetic studies is based on samples of both genes and taxa. In an ideal world, with no limitations to resources, as many genes could be sampled as deemed necessary to address phylogenetic problems. Given limited resources in the real world, inadequate (in terms of choice of genes or number of genes) sequences or restricted taxon sampling can adversely affect the reliability or information gained in phylogenetics. Recent empirical and simulation-based studies of data sampling in molecular phylogenetics have reached differing conclusions on how to deal with these problems. Some advocated sampling more genes, others more taxa. There is certainly no ‘magic bullet’ that will fit all phylogenetic problems, and no specific ‘golden rules’ have been deduced, other than that single genes may not always contain sufficient phylogenetic information. However, several general conclusions and suggestions can be made. One suggestion is that the determination of a multiple, but moderate number (e.g., 6–10) of gene sequences might take precedence over sequencing a larger set of genes and thereby permit the sampling of more taxa for a phylogenetic study.     

Variance estimation for systematic designs in spatial surveys

Summary In spatial surveys for estimating the density of objects in a survey region, systematic designs will generally yield lower variance than random designs. However, estimating the systematic variance is well known to be a difficult problem. Existing methods tend to overestimate the variance, so although the variance is genuinely reduced, it is over‐reported, and the gain from the more efficient design is lost. The current approaches to estimating a systematic variance for spatial surveys are to approximate the systematic design by a random design, or approximate it by a stratified design. Previous work has shown that approximation by a random design can perform very poorly, while approximation by a stratified design is an improvement but can still be severely biased in some situations. We develop a new estimator based on modeling the encounter process over space. The new “striplet” estimator has negligible bias and excellent precision in a wide range of simulation scenarios, including strip‐sampling, distance‐sampling, and quadrat‐sampling surveys, and including populations that are highly trended or have strong aggregation of objects. We apply the new estimator to survey data for the spotted hyena (Crocuta crocuta) in the Serengeti National Park, Tanzania, and find that the reported coefficient of variation for estimated density is 20% using approximation by a random design, 17% using approximation by a stratified design, and 11% using the new striplet estimator. This large reduction in reported variance is verified by simulation.     

Evaluation of different observational sampling regimes for use in zoological parks

Observational sampling methods provide clearly-defined guidelines for collection and analysis of behavioral data. In some situations, use of formal sampling regimes may be impractical or impossible. A case in point is data collection conducted by animal care staff at zoological parks and aquaria. Often, time is sufficiently limited that data collection is perceived as a task that cannot be accomplished given the normal constraints of the day. Here, we explore the efficacy and validity of using more variable and abridged sampling regimes in an effort to identify the appropriateness of such observation schemes for systematic monitoring of behavior. We describe the results of studies on three species (two polar bears, an Atlantic bottlenose dolphin calf, and two brown bears), conducted over a period of several years at the Brookfield Zoo, Brookfield, Illinois, USA. Data collection schemes varied both within and across groups in order to provide a basis of comparison. In all cases, there were significant differences based on sampling regime for rare behaviors (those that individually comprised <15% of the activity budget), but not for common behaviors. Subsampling from larger data sets indicated that data reliability increases with increasing observation number. We discuss the strengths and weaknesses of such sporadic sampling methods, and suggest that, in many instances such limited data collection may yet yield an accurate picture of animal activity and should not be overlooked as a viable management tool.     

A dispersal-limited sampling theory for species and alleles

The importance of dispersal for biodiversity has long been recognized. However, it was never advertised as vigorously as Stephen Hubbell did in the context of his neutral community theory. After his book appeared in 2001, several scientists have sought and found analytical expressions for the effect of dispersal limitation on community composition, still in the neutral context. This has been done along two relatively independent lines of research that have a different mathematical approach and focus on different, yet related, types of results. Here, we study both types in a new framework that makes use of the sampling nature of the theory. We present sampling distributions that contain binomial or hypergeometric sampling on the one hand, and dispersal limitation on the other, and thus views dispersal limitation as ubiquitous as sampling effects. Further, we express the results of one line of research in terms of the other and vice versa, using the concept of subsamples. A consequence of our findings is that metacommunity size does not independently affect the outcome of neutral models in contrast to a previous assertion (Ecol. Lett., 7, 2004, p. 904) based on an incorrect formula (Phys. Rev. E, 68, 2003, p. 061902, eqns 11-14). Our framework provides the basis for development of a dispersal-limited non-neutral community theory and applies in population genetics as well, where alleles and mutation play the roles of species and speciation respectively.     

油松毛虫(Dendrolimus labulaeformis)幼虫抽样技术的研究

本文在测定油松毛虫幼虫静态格局和动态格局的条件下,全面而系统地进行了株抽样、轮抽样和“枝”抽样的研究。根据幼虫在各轮垂直分布的特征和喜食二年生针叶的特性,建立回归模型,从轮抽样发展到“枝”抽样,通过检验,预报精度在91—98％之间。轮抽样比株抽样平均提高效率6倍,“枝”抽样比轮抽样又平均提高1.5倍。如费用以每株0.20元计,轮抽样比株抽样每株平均减少0.16元,“枝”抽样每株又减少0.032元。     

Ranked set sampling for replicated sampling designs

In practical ecological sampling studies, a certain design (such as plot sampling or line-intercept sampling) is usually replicated more than once. For each replication, the Horvitz-Thompson estimation of the objective parameter is considered. Finally, an overall estimator is achieved by averaging the single Horvitz-Thompson estimators. Because the design replications are drawn independently and under the same conditions, the overall estimator is simply the sample mean of the Horvitz-Thompson estimators under simple random sampling. This procedure may be wisely improved by using ranked set sampling. Hence, we propose the replicated protocol under ranked set sampling, which gives rise to a more accurate estimation than the replicated protocol under simple random sampling.     

A floatable,benthic corer for use with scuba

A diver-operated corer to sample benthic macroinvertebrates is described. Removable drive-handles allow the 9-cm (ID) barrel to be driven into substrates too firm to be sampled by line-held or conventional diver-operated corers. The sampler is emptied underwater using compressed air and its buoyancy can be controlled by filling a rubber inner tube.This study was supported by the Pennsylvania Power and Light Company     

A comparison of pump sampling systems for live zooplankton collection

Simultaneous and sequential tests of pump sampling equipment showed that sampling mortality of Lake Michigan zooplankton collected from the cooling water intake of a nuclear power plant was dependent on the sampling method used. Two sampling devices and two pump types were tested to determine which combination resulted in the lowest sampling mortality. An in-line filter trap located on the suction side of the pump provided the lowest sampling mortality. Higher sampling rates were achieved with a centrifugal pump without increasing sampling mortality.     

不同采样设计评估鱼类群落效果比较

鱼类群落生态学研究结果的准确性很大程度上依赖于采样设计的合理性和准确性,正确的采样调查设计不仅可以降低调查成本,其结果也对渔业资源的评估或者管理起到相当重要的作用.本文利用计算机模拟定点采样、简单随机采样和分层采样,比较了3种采样设计的采样效果、相对误差及相对偏差.结果表明： 定点采样设计的采样效果 (采样效果平均值为3.37)要弱于简单随机采样和分层随机采样 (采样效果平均值为0.961).3种采样设计中,分层采样设计在鱼类群落丰富度评估时表现最好,其采样效果、相对误差和相对偏差表现最佳.随着采样数的增加,分层采样设计的采样效果有所下降,但其采样精度提高.