Demerelate: calculating interindividual relatedness for kinship analysis based on codominant diploid genetic markers using R

The Demerelate package offers algorithms to calculate different interindividual relatedness measurements. Three different allele sharing indices, five pairwise weighted estimates of relatedness and four pairwise weighted estimates with sample size correction are implemented to analyse kinship structures within populations. Statistics are based on randomization tests; modelling relatedness coefficients by logistic regression, modelling relatedness with geographic distance by mantel correlation and comparing mean relatedness between populations using pairwise t‐tests. Demerelate provides an advance on previous software packages by including some estimators not available in R to date, along with F_IS, as well as combining analysis of relatedness and spatial structuring. An UPGMA tree visualizes genetic relatedness among individuals. Additionally, Demerelate summarizes information on data sets (allele vs. genotype frequencies; heterozygosity; F_IS values). Demerelate is – to our knowledge – the first R package implementing basic allele sharing indices such as Blouin's M_xy relatedness, the estimator of Wang corrected for sample size (wang_xy), estimators based on Morans I adapted to genetic relatedness as well as combining all estimators with geographic information. The R environment enables users to better understand relatedness within populations due to the flexibility of Demerelate of accepting different data sets as empirical data, reference data, geographical data and by providing intermediate results. Each statistic and tool can be used separately, which helps to understand the suitability of the data for relatedness analysis, and can be easily implemented in custom pipelines.     

Our better nature: Does resource stress predict beyond-household sharing?

Food sharing and (to a lesser extent) labor sharing play central roles in the evolution of cooperation literature. One popular explanation for sharing beyond the family is that it reduces the likelihood of shortages by pooling risk across households. However, the frequency and scope of sharing have never been systematically documented across nonindustrial societies, and the literature is driven by theoretical models, experimental games, and case studies among a few extensively-studied populations. Here we explore the cross-cultural context, frequency, and scope of food and labor sharing customs in relation to resource stress. Using ethnographic data from a worldwide sample of 98 societies in the Standard Cross-Cultural Sample (SCCS), we test the following hypotheses: 1) customary sharing of food and labor beyond the household are cultural universals, 2) societies subject to more resource stress (including unpredictable food-destroying natural hazards) will share more frequently, and 3) the more frequent the resource stress, the broader the geographic and social scope of sharing customs. Hypotheses 1 and 2 are generally supported and are consistent with the theory that extensive beyond-household sharing is adaptive in societies that are subject to more resource stress. Hypothesis 3 was not supported and, contrary to our predictions, there is suggestive evidence that sharing beyond-relatives may be attenuated when resource stress is high. In light of these findings, we consider how resource stress may constitute an important selection pressure for maintaining extensive cooperation and help to explain the ubiquity of beyond-household sharing.     

Women in developing countries and benefit sharing

The aim of this paper is to show that any process of benefit sharing that does not guarantee the representation and participation of women in the decision-making process, as well as in the distribution of benefits, contravenes a central demand of social justice. It is argued that women, particularly in developing countries, can be excluded from benefits derived from genetic research because of existing social structures that promote and maintain discrimination. The paper describes how the structural problem of gender-based inequity can impact on benefit sharing processes. At the same time, examples are given of poor women's ability to organise themselves and to achieve social benefits for entire communities. Relevant international guidelines (e.g. the Convention on Biodiversity) recognise the importance of women's contributions to the protection of biodiversity and thereby, implicitly, their right to a share of the benefits, but no mechanism is outlined on how to bring this about. The authors make a clear recommendation to ensure women's participation in benefit sharing negotiations by demanding seats at the negotiation table.     

Getting a Fair Share: Attitudes and Perceptions of Biobank Stakeholders Concerning the Fairness of Sample Sharing

Biobanks are essential tools for furthering a broad range of medical research areas. However, despite the plethora of national and international laws and guidelines which apply to them, the access and sharing policies of biobanks are only sparsely addressed by regulatory bodies. The ‘give and take’ process of biosample sharing is largely left up to biobank stakeholders themselves to oversee; it is therefore both in stakeholders' power, and in their interest, to ensure that sample accessibility is fair. This is an important step in motivating researchers to collaborate and pool samples, and is crucial to fostering trust in the absence of universally accepted standard practices. To date, little attention has been paid to how fairness considerations affect scientific material sharing, and no empirical research has been carried out to determine the role that fairness plays in collaborative studies. In order to begin to gain understanding in this area, we interviewed 36 biobank stakeholders currently working in Switzerland, focusing on their perceptions of current and optimal fair sharing practices. Our findings reveal that fairness is an important feature of exchange situations for these stakeholders, and that they have well‐formed notions about the practical elements of fair sample access, although ideas about the concept of fairness itself are vague. In order to support efforts to network biobanks, attention should be paid to this issue to reassure all involved that they are getting a fair share in their cooperative efforts.     

North-South benefit sharing arrangements in bioprospecting and genetic research: a critical ethical and legal analysis

Most pharmaceutical research carried out today is focused on the treatment and management of the lifestyle diseases of the developed world. Diseases that affect mainly poor people are neglected in research advancements in treatment because they cannot generate large financial returns on research and development costs. Benefit sharing arrangements for the use of indigenous resources and genetic research could only marginally address this gap in research and development in diseases that affect the poor. Benefit sharing as a strategy is conceptually problematic, even if one, as we do, agrees that impoverished indigenous communities should not be exploited and that they should be assisted in improving their living conditions. The accepted concept of intellectual property protection envisages clearly defined originators and owners of knowledge, whereas the concept of community membership is fluid and indigenous knowledge is, by its very nature, open, with the originator(s) lost in the mists of time. The delineation of 'community' presents serious conceptual and practical difficulties as few communities form discrete, easily discernable groups, and most have problematic leadership structures. Benefit sharing is no substitute for governments' responsibility to uplift impoverished communities. Benefit sharing arrangements may be fraught with difficulties but considerations of respect and equity demand that prior informed consent and consultation around commercialisation of knowledge take place with the source community and their government.     

The care of infants in a wild marmoset (Callithrix flaviceps) group

The behavior of a free-ranging group of buffy-headed marmosets (Callithrix flaviceps) was observed in detail over a five-month period following the birth of twins. Infant care, principally carrying and food sharing, were analyzed and the variation both between age-sex classes and through time investigated. Potentially reproductive males exhibited a relatively high degree of interest in the infants during the first week following birth, but their provision of care was otherwise little different from that of other group members. The data are considered in relation to the factors stimulating care-giving behavior and possible differences between callitrichid genera are discussed.     

生物多样性数据集成模式初探

本文以生物多样性研究发展现状的分析为基础,为生物多样性保护政策的制定提供可靠的数据支持为目标,通过对国内外几个著名的生物多样性数据库建设情况的分析,从相关学者的需求出发,提出了设计一个多层次多角度并带有一定人工智能的生物多样性集成数据库的构想。该系统基于都柏林核心(Dublin Core)的数据规范,并符合基于开放文献预研的元数据互操作协议(The Open Archixles Initiative Protocol for Metadata Hatvesting,OAIPMH)的标准,是一个集文字、图件、图片、声音、影像为一体的,能够在网上和硬件载体(如光盘)上同时进行发布的分布式数据库平台。其网上数据库系统的子系统之间以及子系统和硬件载体之间可以通过元数据获取的开放档案倡议协议互相交换数据。     

Open resource metagenomics: a model for sharing metagenomic libraries

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM²BL [1]). The CM²BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.     

Data sharing across biobanks: epistemic values,data mutability and data incommensurability

Despite the centrality of epistemic issues in biobank knowledge generation, there is currently a lacuna in research addressing the epistemic assumptions of biobank science and data sharing. The article addresses this lacuna. Using the insights of philosophical and sociological analysis, we examine standardization and harmonization and central challenges biobank data-sharing faces. We defend two central epistemic values, namely “spatial and temporal translatability” and “epistemic adequacy” which foster effective biobank knowledge generation. The first refers to the way in which biobank data need to be re-usable and re-purposable by bioscience researchers who did not create them. Given the perennial issues of data mutability and incommensurability, we also propose “epistemic adequacy.” In uncovering the social and epistemic foundations of biobank science, we emphasize issues essential for achieving effective and transparent biobank practice and productive communication and engagement with the public about the nature, potential and limits of biobanks.     

《生物多样性公约》对遗传资源国际交流政策的影响

《生物多样性公约》于1992年在巴西里约热内卢签订,1993年生效。该公约提出了“国家对生物遗传资源拥有主权、获取生物遗传资源须事先得到资源所有者的知情同意、利用生物遗传资源所产生的利益应由资源所有者和开发者公平分享”三项基本原则,其生效与实施促进了各国生物多样性保护的立法行动,在维护资源原产国利益方面发挥了积极的作用,同时也给遗传资源的国际交流增添了一些障碍。本文介绍了《生物多样性公约》中有关生物遗传资源获取和利益分享的条款及其对国际交流政策的影响,并提出了加强遗传资源国际交换的对策和建议。     

水分共享在毛乌素沙地4种灌木根系中的存在状况

为揭示水分共享在毛乌素沙化草地4种沙生灌木根系中的存在状况,选择酸性品红为示踪剂开展野外实验。结果表明,只有沙地柏（Sabina vulgaris)和油蒿（Artemisia ordosica）根系具有共享水分的潜力,而沙柳Salix psammophaila)和杨柴（Hedysarum mongolicum)根系不具有这种潜力。基于酸性品红在细根中的存在状况以及沙子与酸性品红发生中和反应,被步认为沙地柏和油蒿根系可能具有提水作用潜力。     

Critical considerations in N-glycoproteomics

N-Glycoproteomics, the system-wide study of glycans asparagine-linked to protein carriers, holds a unique and still largely untapped potential to provide deep insights into the complexity and dynamics of the heterogeneous N-glycoproteome. Despite the advent of innovative analytical and informatics tools aiding the analysis, N-glycoproteomics remains challenging and consequently largely restricted to specialised laboratories. Aiming to stimulate discussions of method harmonisation, data standardisation and reporting guidelines to make N-glycoproteomics more reproducible and accessible to the community, we here discuss critical considerations related to the design and execution of N-glycoproteomics experiments and highlight good practices in N-glycopeptide data collection, analysis, interpretation and sharing. Giving the rapid maturation and, expectedly, a wide-spread implementation of N-glycoproteomics capabilities across the community in future years, this piece aims to point out common pitfalls, to encourage good data sharing and documentation practices, and to highlight practical solutions and strategies to enhance the insight into the N-glycoproteome.     

Reservation food sharing among the Ache of Paraguay

We describe food transfer patterns among Ache Indians living on a permanent reservation. The social atmosphere at the reservation is characterized by a larger group size, a more predictable diet, and more privacy than the Ache typically experience in the forest while on temporary foraging treks. Although sharing patterns vary by resource type and package size, much of the food available at the reservation is given to members of just a few other families. We find significant positive correlations between amounts transferred among pairs of families, a measure of the "contingency" component required of reciprocal altruism models. These preferred sharing partners are usually close kin. We explore implications of these results in light of predictions from current sharing models. This research was supported by an L.S.B. Leakey Foundation grant and an NSF Graduate Fellowship to M. Gurven, and NSF Grant #9617692 to K. Hill and A. M. Hurtado. Michael Gurven recently obtained his Ph.D. from the University of New Mexico and is now an assistant professor at UC-Santa Barbara. His current interests include exploring ways in which socioecology influences variation in cooperation within and across human groups, and how cultural norms of fairness co-evolve with systems of resource production and distribution. Wesley Allen-Arave is pursuing his Ph.D. in anthropology at the University of New Mexico. His primary research interests focus on exploring variations across time and space in nonreciprocated altruistic acts, cooperation within social networks, and concerns over social approval. Kim Hill is a professor of anthropology in the Human Evolutionary Ecology (HEE) program at the University of New Mexico. His primary research interests include hunter-gatherer behavioral ecology, life history theory, food acquisition strategies, food sharing, cooperation, and biodiversity conservation in lowland South America. He has done fieldwork with Nahautl, Ache, Guarani, Hiwi, Mashco Piro, Matsiguenga, and Yora indigenous peoples of Central and South America. A. Magdalena Hurtado is associate professor of anthropology at the University of New Mexico. Her research interests include the evolution of cooperation between the sexes, infectious disease and immune system adaptations, the epidemiology of hunter-gatherer societies in transition, and the effects of health on economic productivity. During the past 20 years she has conducted fieldwork among several South American native populations but now works primarily among the Ache of eastern Paraguay.     

Why do good hunters have higher reproductive success?

Anecdotal evidence from many hunter-gatherer societies suggests that successful hunters experience higher prestige and greater reproductive success. Detailed quantitative data on these patterns are now available for five widely dispersed cases (Ache, Hadza, !Kung, Lamalera, and Meriam) and indicate that better hunters exhibit higher age-corrected reproductive success than other men in their social group. Leading explanations to account for this pattern are: (1) direct provisioning of hunters’ wives and offspring, (2) dyadic reciprocity, (3) indirect reciprocity, (4) costly signaling, and (5) phenotypic correlation. I examine the qualitative and quantitative evidence bearing on these explanations and conclude that although none can be definitively rejected, extensive and apparently unconditional sharing of large game somewhat weakens the first three explanations. The costly signaling explanation has support in some cases, although the exact nature of the benefits gained from mating or allying with or deferring to better hunters needs further study. For comments on earlier drafts, I thank Monique Borgerhoff Mulder, Mike Gurven, Ray Hames, Kristen Hawkes, Kim Hill, Robert Kelly, Frank Marlowe, John Patton, and Polly Wiessner. Rebecca Bliege Bird and Douglas W. Bird invited me to collaborate in the Meriam research and (along with Del Passi of Mer) collected the data on Meriam demography. Geoff Kushnick and Matt Wimmer ably assisted with coding and statistical analysis of these data. Eric Alden Smith (PhD 1980, Cornell University) is a professor of anthropology at the University of Washington, Seattle. His research interests include the links between production and reproduction, the ecology and evolution of collective action, and politics in small-scale societies. He has conducted fieldwork among Inuit on Hudson Bay, Meriam in Torres Strait, and Mardu Aborigines in the Australian Western Desert.     

植物标本信息共享与整合——以广西植物标本馆为例

以植物标本资源整合共享为主线,寻求和探索"信息孤岛"现象的原因,进一步体现共享整合的价值。通过开展深入调研,找出存在的问题和原因,并采取灵活多样的整合方式和共享模式,来实现植物标本信息资源的高效利用。     

基于省级平台的临床路径知识库共享平台设计

提出了一种基于省级平台的临床路径知识库共享系统的设计方案,主要从系统整体架构的设计、网络结构设计、功能规划以及系统的业务流程设计几个方面进行了分析。构架基于省级平台的临床知识库共享平台,可以将过去单一的仅在本医院内使用的临床路径分享给所有医院,真正意义上实现数据互通,数据共享。同时,本系统与省外医疗信息平台实现对接。     

杭州春季常见庭园鸟类的晨鸣时序和频域特征

对杭州春季（3－5月）5种庭园常见鸟的晨鸣做定点和定个体录音,然后用计算机声谱分析系统处理录音。结果表明：同域鸟类的晨鸣有一定的时序;乌鸫最早鸣叫,而大山雀、白头鹎和鹊鸲的始鸣时序有月间变化。5种鸟晨鸣的主频集中在2.4-4.1kHz;除了鹊鸲和麻雀无差异外,其余均有极显著差异;这种差异为进一步研究群落内种间频域竞争提供了部分基础资料。