Capture-recapture, epidemiology, and list mismatches: two lists

In recent years, capture-recapture methods for closed populations have been extensively applied to epidemiology. For example, suppose we have several incomplete lists of diabetics and we wish to estimate the total number of diabetics by estimating the number missing from all the lists. A major problem is that the information about individuals on the lists may have been given incorrectly or the information may have been typed incorrectly so that some list matches are missed. Using the concept of tag loss borrowed from animal population studies, we consider methods for estimating both the probabilities of making list errors and the population size for just two independent lists. The effect of heterogeneity on the errors is examined. The methods are applied to a large data set of diabetic persons consisting of a list obtained from a survey and a list obtained from doctors' records. It was found that the error rates were high and that ignoring the errors led to a gross overestimate of the total number of diabetic persons.     

国家濒危物种红色名录的生物多样性保护意义

IUCN濒危物种红色名录与国家濒危物种红色名录都是物种灭绝风险的测度, 前者是全球性评估, 后者则是国别研究。IUCN濒危物种红色名录预警了全球物种的濒危状况, 为全球生物多样性研究提供了大数据; 国别红色名录确定了各国物种受威胁状况, 填补了前者的知识空缺, 两份名录互为补充。目前对国家濒危物种红色名录重视不够。基于如下原因, 应当重视国别濒危物种红色名录的意义: (1)国家是濒危物种保护的行为主体, 物种在一个国家的生存状况是确定其保护级别、开展濒危物种保育的依据; (2)对于仅分布于一个国家的特有物种来说, 其国别濒危物种红色名录等级即是其全球濒危等级; (3)对于跨国境分布的物种来说, 国别濒危物种红色名录等级则确定了该物种在本国的生存状况; (4)结合IUCN濒危物种红色名录, 国别濒危物种红色名录为建立跨国保护地、保护迁徙物种的栖息地与跨国迁徙洄游通道提供依据; (5)国别濒危物种红色名录所特有的“区域灭绝”等级, 反映了一个物种边缘种群在该国的区域灭绝, 恢复“区域灭绝”物种是该物种原分布国重引入保育工作的重点; (6)国别濒危物种红色名录提供了该国物种编目、分类、分布和生存状况的最新信息。然而, 国别濒危物种红色名录的重要性在许多情况下被忽视了。目前正值全球新冠肺炎大流行, 人们正在重新审视人与野生动物的关系。我国将修订有关野生动物保护与防疫法法律以及《国家重点保护野生动物名录》, 防控新的人与野生动物共患疾病再次暴发。对于确定国家重点保护野生动物物种名录来言, 物种受威胁程度是物种列为国家重点保护物种的特征之一。重视国别红色名录有特别的意义。     

Effect of list errors on the estimation of population size

In many situations, it is possible to estimate the size of a closed population if some members of the population are recorded on one or more administrative lists. An important example is estimating the prevalence of a disease, where some members of the disease population may be recorded on lists such as disease registries, hospital admission records, and general practitioner records. An incomplete contingency table is formed by matching the lists and the missing cell count estimated by prediction based on a fitted model, which assumes that the matching is done without error. In practice, matching errors do occur, and in this article, we examine the effect of these errors on the estimation process and show how the standard models may be modified to allow for matching errors.     

MutS recognition: Multiple mismatches and sequence context effects

Escherichia coli MutS is a versatile repair protein that specifically recognizes not only various types of mismatches but also single stranded loops of up to 4 nucleotides in length. Specific binding, followed by the next step of tracking the DNA helix that locates hemi-methylated sites, is regulated by the conformational state of the protein as a function of ATP binding/hydrolysis. Here, we study how various molecular determinants of a heteroduplex regulate mismatch recognition by MutS, the critical first step of mismatch repair. Using classical DNase I footprinting assays, we demonstrate that the hierarchy of MutS binding to various types of mismatches is identical whether the mismatches are present singly or in multiples. Moreover, this unique hierarchy is indifferent both to the differential level of DNA helical flexibility and to the unpaired status of the mismatched bases in a heteroduplex. Surprisingly, multiple mismatches exhibit reduced affinity of binding to MutS, compared to that of a similar single mismatch. Such a reduction in the affinity might be due to sequence context effects, which we established more directly by studying two identical single mismatches in an altered sequence background. A mismatch, upon simply being flipped at the same location, elicits changes in MutS specific contacts, thereby underscoring the importance of sequence context in modulating MutS binding to mismatches.     

生态系统红色名录——一种新的生物多样性保护工具

生物多样性为人类提供了生存所必需的一系列生态系统服务和功能。然而,由于人为活动的加剧,生物多样性不断丧失。传统的生物多样性保护主要关注物种多样性,存在着对生物多样性的代表性不足,不能及时反应生态系统多样性的变化等缺点。近年来,生态系统层次上的多样性保护成为研究热点,一些国家和组织相继开展了大尺度的生态系统评估工作。文章回顾了已有的生态系统评估方案,发现当前生态系统评估多采用IUCN物种红色名录的分级标准体系,主要评估生态系统的濒危程度,评估标准主要是分布范围和功能的变化,不同评估方案采用的指标和阈值有差异,需要建立统一的生态系统分类体系和评价方案。同时,结合国内生态系统评价的现状,提出了在我国开展生态系统红色名录研究的若干可行建议。     

The assessment of arboreal insect fauna: comparisons of knockdown sampling and faunal lists

Abstract. 1. A comparison is made between the fauna of six British tree species sampled by pyrethrum knockdown and the faunal lists in the literature for the same tree species.
2. Conspecific trees vary both in abundance of arthropods and their proportional distribution across taxa, but there are important overriding differences between tree species.
3. The percentage similarity in faunal composition between tree species reflects the ecological specificity of the arthropod groups used for the comparison.
4. The similarity in species composition between tree species is least for phytophages, the guild most closely associated with particular tree species, The two species of Salix are most similar in their fauna for most guilds.
5. About 40% of the entirely phytophagous species in the faunal lists for native trees were found in the knockdown samples.
6. The proportion of individuals of predominantly phytophagous taxa collected that belong to the relevant faunal lists ranges from 0.39 to 0.99.
7. Those species found in the knockdown samples which are not included in faunal lists none the less contribute to the trophic web of the tree.
8. The relative species richness of arboreal faunas assessed from knockdown samples parallels that derived from faunal lists.
9. The two approaches to the categorization of arboreal faunas, knockdown sampling and faunal lists, provide comparable data.     

The influence of environmental variables on capybara (Hydrochoerus hydrochaeris: Rodentia, Hydrochoeridae) detectability in anthropogenic environments of southeastern Brazil

Capybaras were monitored weekly from 1998 to 2006 by counting individuals in three anthropogenic environments (mixed agricultural fields, forest and open areas) of southeastern Brazil in order to examine the possible influence of environmental variables (temperature, humidity, wind speed, precipitation and global radiation) on the detectability of this species. There was consistent seasonality in the number of capybaras in the study area, with a specific seasonal pattern in each area. Log-linear models were fitted to the sample counts of adult capybaras separately for each sampled area, with an allowance for monthly effects, time trends and the effects of environmental variables. Log-linear models containing effects for the months of the year and a quartic time trend were highly significant. The effects of environmental variables on sample counts were different in each type of environment. As environmental variables affect capybara detectability, they should be considered in future species survey/monitoring programs.     

A list of personal perspectives with selected quotations,along with lists of tributes,historical notes,Nobel and Kettering awards related to photosynthesis

The history of photosynthesis research can be found in original papers and books. However, a special history is available from the prefatory chapters and the personal perspectives of various researchers who published them in several journals over the last 40 years. We have compiled a list of such perspectives published since 1964. Selection is not easy, especially of authors who were not directly engaged in photosynthesis research; some are included for their special insights related to central issues in the study of photosynthesis. Our journal, Photosynthesis Research, contains other valuable historic data in the occasional tributes, obituaries and historical notes, that have been published. Lists of these items are included. This article ends by listing the Nobel prizes related to photosynthesis and the Kettering Awards for Excellence in Photosynthesis Research. Wherever possible, a web page address is provided. The web page addresses have been taken from the article `Photosynthesis and the Web: 2001' by Larry Orr and Govindjee, available at http://www.life.uiuc.edu/govindjee/photoweb and at http://photoscience.la.asu.edu/photosyn/ photoweb/default.html. ‘When I find a bit of leisure I trifle with my papers. This is one of the lesser frailities. – Horace, Satires I, IV. This revised version was published online in June 2006 with corrections to the Cover Date.     

Analysis of in vivo correction of defined mismatches in the DNA mismatch repair mutants msh2 , msh3 and msh6 of Saccharomyces cerevisiae

We have analysed the correction of defined mismatches in wild-type and msh2, msh3, msh6 and msh3 msh6 mutants of Saccharomyces cerevisiae in two different yeast strain backgrounds by transformation with plasmid heteroduplex DNA constructs. Ten different base/base mismatches, two single-nucleotide loops and a 38-nucleotide loop were tested. Repair of all types of mismatches was severely impaired in msh2 and msh3 msh6 mutants. In msh6 mutants, repair efficiency of most base/base mismatches was reduced to a similar extent as in msh3 msh6 double mutants. G/T and A/C mismatches, however, displayed residual repair in msh6 mutants in one strain background, implying a role for Msh3p in recognition of base/base mismatches. Furthermore, the efficiency of repair of base/base mismatches was considerably reduced in msh3 mutants in one strain background, indicating a requirement for MSH3 for fully efficient mismatch correction. Also the efficiency of repair of the 38-nucleotide loop was reduced in msh3 mutants, and to a lesser extent in msh6 mutants. The single-nucleotide loop with an unpaired A was less efficiently repaired in msh3 mutants and that with an unpaired T was less efficiently corrected in msh6 mutants, indicating non-redundant functions for the two proteins in the recognition of single-nucleotide loops. Received: 7 August 1997 / Accepted: 24 September 1997     

Climate‐driven spatial mismatches between British orchards and their pollinators: increased risks of pollination deficits

Understanding how climate change can affect crop‐pollinator systems helps predict potential geographical mismatches between a crop and its pollinators, and therefore identify areas vulnerable to loss of pollination services. We examined the distribution of orchard species (apples, pears, plums and other top fruits) and their pollinators in Great Britain, for present and future climatic conditions projected for 2050 under the SRES A1B Emissions Scenario. We used a relative index of pollinator availability as a proxy for pollination service. At present, there is a large spatial overlap between orchards and their pollinators, but predictions for 2050 revealed that the most suitable areas for orchards corresponded to low pollinator availability. However, we found that pollinator availability may persist in areas currently used for fruit production, which are predicted to provide suboptimal environmental suitability for orchard species in the future. Our results may be used to identify mitigation options to safeguard orchard production against the risk of pollination failure in Great Britain over the next 50 years; for instance, choosing fruit tree varieties that are adapted to future climatic conditions, or boosting wild pollinators through improving landscape resources. Our approach can be readily applied to other regions and crop systems, and expanded to include different climatic scenarios.     

Aegilops (Poaceae) in Italy: taxonomy,geographical distribution,ecology, vulnerability and conservation

ABSTRACT

Aegilops L. includes wild species from which, over millennia, man has cultivated forms of Triticum L. Ten species of Aegilops occur in Italy. Three species are allochthonous and eight out of ten species are recorded in the Apulia region. Five out of the ten species have been included in Red Lists. Each taxon is presented and discussed, citing old and new sites of occurrence, by examining specimens from many different herbaria, and describing their ecology and habitats, according to the Directive 92/43 EEC. A new taxonomic key, for the identification of all Aegilops species growing in Italy, is provided. The occurrence of Aegilops caudata L., A. peregrina (Hack. in J. Fraser) Maire & Weiller and A. speltoides Tausch in Italy is doubtful.     

Four mismatch repair paralogues coexist in Arabidopsis thaliana : AtMSH2, AtMSH3, AtMSH6-1 and AtMSH6-2

By using degenerate oligonucleotides based on the sequence homology between known MutS homologues, three MSH cDNAs belonging to the MSH2, MSH3 and MSH6 families, as defined in eukaryotes, have been isolated from Arabidopsis thaliana (ecotype Columbia). Genomic sequences for two of these genes (AtMSH2 and AtMSH6-2) were also isolated and determined, whereas the genomic sequence of AtMSH3 was obtained through the Arabidopsis sequencing project, as was the sequence of a second, distinct AtMSH6 homologue (AtMSH6-1). Comparative analysis of the AtMSH2 Landsberg erecta genomic sequence (reported here) and the previously described AtMSH2 Columbia allele revealed several polymorphisms, including the presence of a small, transposon-like element in the 3′ untranscribed region of the former allele. Arabidopsis is the first organism to show such divergence of two AtMSH6 genes; the divergence is strongly supported by sequence data and phylogenetic analysis. Southern analysis revealed that the three genes we have isolated exist as single copies, and genetic mapping indicated that AtMSH2 and AtMSH6-2 both reside on chromosome III. Finally, expression of these three genes could only be observed in suspensions of A. thaliana cells. Such a cell suspension divides actively after subculture, and the AtMSH genes are most strongly expressed at this stage. Received: 23 February 1999 / Accepted: 5 May 1999     

Endemic cattle diseases: comparative epidemiology and governance

Cattle are infected by a community of endemic pathogens with different epidemiological properties that invoke different managerial and governmental responses. We present characteristics of pathogens that influence their ability to persist in the UK, and describe a qualitative framework of factors that influence the political response to a livestock disease. We develop simple transmission models for three pathogens (bovine viral diarrhoea virus, bovine herpesvirus and Mycobacterium avium spp. paratuberculosis) using observed cattle movements, and compare the outcomes to an extensive dataset. The results demonstrate that the epidemiology of the three pathogens is determined by different aspects of within- and between-farm processes, which has economic, legal and political implications for control. We consider how these pathogens, and Mycobacterium bovis (the agent of bovine tuberculosis), may be classified by the process by which they persist and by their political profile. We further consider the dynamic interaction of these classifications with pathogen prevalence and with the action taken by the government.     

Multi-species occupancy models: review,roadmap, and recommendations

Recent technological and methodological advances have revolutionized wildlife monitoring. Although most biodiversity monitoring initiatives are geared towards focal species of conservation concern, researchers are increasingly studying entire communities, specifically the spatiotemporal drivers of community size and structure and interactions among species. This has resulted in the emergence of multi-species occupancy models (MSOMs) as a promising and efficient approach for the study of community ecology. Given the potential of MSOMs for conservation and management action, it is critical to know whether study design and model assumptions are consistent with inference objectives. This is especially true for studies that are designed for a focal species but can give insights about a community. Here, we review the recent literature on MSOMs, identify areas of improvement in the multi-species study workflow, and provide a reference model for best practices for focal species and community monitoring study design. We reviewed 92 studies published between 2009 and early 2018, spanning 27 countries and a variety of taxa. There is a consistent under-reporting of details that are central to determining the adequacy of designs for generating data that can be used to make inferences about community-level patterns of occupancy, including the spatial and temporal extent, types of detectors used, covariates considered, and choice of field methods and statistical tools. This reporting bias could consequently result in skewed estimates, affecting conservation actions and management plans. On the other hand, comprehensive reporting is likely to help researchers working on MSOMs assess the robustness of inferences, in addition to making strides in terms of reproducibility and reusability of data. We use our literature review to inform a roadmap with best practices for MSOM studies, from simulations to design considerations and reporting, for the collection of new data as well as those involving existing datasets.     

Red-listed lichens in Sweden: habitats, threats, protection, and indicator value in boreal coniferous forests

The three major threats to lichens in Sweden; forestry, air pollution, and structural changes in the agricultural landscape, are outlined. Forestry is the most serious. The majority of the red-listed lichens in forests are found in productive forests with a continuity in tree growth, but nearly 70% of the protected area in Sweden consists of alpine landscapes. Examples of important habitats with red-listed lichens are described, e.g. Alnus glutinosa marshes, alvar-vegetation, broad-leaved deciduous forests and different Picea abies forests. The use of selected indicator species of lichens and macrofungi (mainly red-listed species) in boreal coniferous forests provides information on continuity in tree growth of an area, and on earlier influences of forestry. Examples of indicator species for different types of forest are presented and discussed. In spite of the Swedish right of common accesso, collecting of lichens is forbidden without permission from the land-owner. Collecting in protected areas is allowed only with a permit obtained from the authorities.     

Ecology,conservation status,and phylogenetic placement of endemic Pristimantis frogs (Anura: Craugastoridae) in Trinidad and Tobago and genetic affinities to northern Venezuela

Trinidad and Tobago are home to three endemic species in the anuran genus Pristimantis, of which two (Pristimantis charlottevillensis and Pristimantis turpinorum) occur in Tobago alone and the third (Pristimantis urichi) is present on both islands. Earlier, the IUCN assessed the conservation status of these species as: P. urichi, Endangered (EN); P. charlottevillensis, Least Concern (LC); P. turpinorum, Vulnerable (VU). However, these assessments were based on very little field-based evidence. Here, we present survey results which contributed to reassessments as LC, VU and Data Deficient for these three species, respectively. Despite the close proximity of Trinidad to northern Venezuela, the islands do not share any Pristimantis species with the mainland, which holds a rich endemicity of Pristimantis regionally. In this study, we used genetic sequencing from several island populations and compared them to northern Venezuelan endemics to assess genetic divergence for the first time. The time tree analyses found that only the northern Tobago species P. turpinorum is closely related to mainland Pristimantis, with a genetic split dating to the Late Miocene, suggesting a vicariant event of mainland and island species. Pristimantis urichi, although identical between the two islands, remains highly divergent from the mainland species. Similar results were found for P. charlottevillensis. In addition, there was a high level of divergence between P. urichi and P. charlottevillensis. These findings indicate different island colonization events by different lineages. Sequencing other Venezuelan species remains pivotal to unravel the complexity of the colonization episodes in the region, likely influenced by the changing topography and multiple connection and isolation episodes of the islands by eustatic sea-level changes.     

物种分布模型在大型真菌红色名录评估及保护中的应用: 以冬虫夏草为例

我国大型真菌资源丰富, 由于受气候变化和人类活动等的影响, 近年来很多物种受到不同程度的威胁, 亟待保护。红色名录评估是物种保护的第一步, 为有效保护我国大型真菌多样性, 2016年生态环境部和中国科学院联合启动中国大型真菌红色名录评估项目。合理的评估依赖于完善的物种地理分布、种群数量规模及其动态变化信息。大型真菌评估信息较少, 需要引入新的方法解决评估信息不足的问题。冬虫夏草(Ophiocordyceps sinensis)是一种重要的食药用菌, 具有较高的经济价值, 受到全世界的广泛关注, 评估信息相对充足, 此次被评为易危物种。利用物种分布模型对冬虫夏草未来分布区变化的预测在评估过程中发挥了重要作用。为了将物种分布模型分析方法引入大型真菌的受威胁等级评估, 本文以此前我们利用物种分布模型预测冬虫夏草的潜在分布区及其对气候变化响应的研究为例, 介绍了应用物种分布模型预测大型真菌的潜在分布区、未来气候变化情景下分布区变化趋势的方法和流程, 以及在应用中可能存在的问题和解决方案。通过本文的分析, 我们认为物种分布模型在大型真菌的红色名录评估和保护中具有重要的应用潜力, 值得推广应用。