芍药属牡丹组（Paeonia sect. Moutan）种间关系的分子证据：GPAT基因的PCR-RFLP和序列分析

为了探讨芍药属牡丹组Paeonia sect. Moutan的种间关系,对采自15个野生居群,代表牡丹组全部8个野生种的15份材料的GPAT 基因片段（外显子5和6之间2 kb的内含子）进行了PCR-RFLP分析,并对代表牡丹组全部8个野生种的9份材料进行了测序。 根据12个限制性内切酶的PCR-RFLP数据,使用Network 3.0计算机程序的RM (reduced-median)法建立了牡丹组种间亲缘关系网络树。同时根据8个种9份材料的GPAT基因片段序列,利用PAUP*4.0计算机程序建立了牡丹组GPAT基因的最大简约（MP）树和邻接(NJ)树。结果获得了具有很高自展值支持、分辨良好的牡丹组种间关系（GPAT基因）树。最重要的是,该基因树所显示的牡丹组种间关系与根据形态学证据提出的牡丹组的种间关系基本吻合,并得到其他研究证据的支持。根据这一结果,对牡丹组的种间关系进行了详细的讨论。     

Can allelopathically active submerged macrophytes stabilise clear-water states in shallow lakes?

Inhibition of phytoplankton by allelochemicals released by submerged macrophytes is supposed to be one of the mechanisms that contribute to the stabilisation of clear-water states in shallow lakes. The relevance of this process at ecosystem level, however, is debated because in situ evidence is difficult to achieve. Our literature review indicates that allelopathically active species such as Myriophyllum, Ceratophyllum, Elodea and Najas or certain charophytes are among the most frequent submerged macrophytes in temperate shallow lakes. The most common experimental approach for allelopathic interference between macrophytes and phytoplankton has been the use of plant extracts or purified plant compounds. Final evidence, however, requires combination with more realistic in situ experiments. Such investigations have successfully been performed with selected species. In situ allelopathic activity is also influenced by the fact that phytoplankton species exhibit differential sensitivity against allelochemicals both between and within major taxonomic groups such as diatoms, cyanobacteria and chlorophytes. In general, epiphytic species apparently are less sensitive towards allelochemicals than phytoplankton despite living closely attached to the plants and being of key importance for macrophyte growth due to their shading. Light and nutrient availability potentially influence the sensitivity of target algae and cyanobacteria. Whether or not additional stressors such as nutrient limitation enhance or dampen allelopathic interactions still has to be clarified. We strongly propose allelopathy as an important mechanism in the interaction between submerged macrophytes and phytoplankton in shallow lakes based on the frequent occurrence of active species and the knowledge of potential target species. The role of allelopathy interfering with epiphyton development is less well understood. Including further levels of complexity, such as nutrient interference, grazing and climate, will extend this ecosystem-based view of in situ allelopathy.     

When Good Lawyers Write Bad History: Unreliable Evidence and the South China Sea Territorial Dispute

The recent award by an arbitral tribunal in a case brought by the Philippines against China gives lawyers reason to reexamine the historical evidence put forward by claimants in the South China Sea disputes. While the Tribunal was barred from considering territorial or boundary questions, it did cast doubt on the historical narrative rule that China has asserted in support of its claims. Fresh evidence from other sources also suggests that discussions of these matters need to move beyond arguments put forward in a small number of papers published more than thirty years ago. A close examination of the references used in those papers shows that they relied upon highly partisan Chinese sources. Recent historical research has produced new facts about the development of the competing territorial claims in the South China Sea, but international legal discourse has yet to take these findings into account. This article examines some of the key works in the field and calls for them to be reassessed and for future discussion of the disputes to be based upon verifiable and contextualized evidence rather than on nationalist assertions.     

Comparative osteology of the Danio (Cyprinidae: Ostariophysi) axial skeleton with comments on Danio relationships based on molecules and morphology

Danio is a diverse group of small, colourful and easily bred freshwater fishes native to Southern Asia. Biological interest in danios has increased in recent years because the zebrafish, Danio rerio , has become an important model organism, particularly for studies of vertebrate developmental biology and genetics. Though several phylogenetic studies of Danio have been done on a subset of Danio species, the resulting phylogenies conflict in detail. To examine the utility of osteology for systematics of this group at the species level, we studied the axial skeleton for 11 species of Danio. We analyse our morphological data alone and combined with DNA sequence data for five gene sequences generated in earlier phylogenetic studies. The axial skeleton of Danio exhibits 14 characters that prove useful in phylogenetic analysis. Both molecular and morphological data support the monophyly of the danios included in our analysis and both data sets support the monophyly of two subclades: a deep-bodied group and a slender-bodied group. Separate analysis of molecular and morphological data sets show that the molecular data resolves relationships within the slender subclade whereas the topology of the deep-bodied subclade is determined by morphological data.  © 2002 The Linnean Society of London. Zoological Journal of the Linnean Society , 2002, 135 , 529–546.     

Irreproducibility in searches of scientific literature: A comparative analysis

1. Repeatability is the cornerstone of science, and it is particularly important for systematic reviews. However, little is known on how researchers’ choice of database, and search platform influence the repeatability of systematic reviews. Here, we aim to unveil how the computer environment and the location where the search was initiated from influence hit results.
2. We present a comparative analysis of time‐synchronized searches at different institutional locations in the world and evaluate the consistency of hits obtained within each of the search terms using different search platforms.
3. We revealed a large variation among search platforms and showed that PubMed and Scopus returned consistent results to identical search strings from different locations. Google Scholar and Web of Science''s Core Collection varied substantially both in the number of returned hits and in the list of individual articles depending on the search location and computing environment. Inconsistency in Web of Science results has most likely emerged from the different licensing packages at different institutions.
4. To maintain scientific integrity and consistency, especially in systematic reviews, action is needed from both the scientific community and scientific search platforms to increase search consistency. Researchers are encouraged to report the search location and the databases used for systematic reviews, and database providers should make search algorithms transparent and revise access rules to titles behind paywalls. Additional options for increasing the repeatability and transparency of systematic reviews are storing both search metadata and hit results in open repositories and using Application Programming Interfaces (APIs) to retrieve standardized, machine‐readable search metadata.

     

A decade of climate change experiments on marine organisms: procedures,patterns and problems

The first decade of the new millennium saw a flurry of experiments to establish a mechanistic understanding of how climate change might transform the global biota, including marine organisms. However, the biophysical properties of the marine environment impose challenges to experiments, which can weaken their inference space. To facilitate strengthening the experimental evidence for possible ecological consequences of climate change, we reviewed the physical, biological and procedural scope of 110 marine climate change experiments published between 2000 and 2009. We found that 65% of these experiments only tested a single climate change factor (warming or acidification), 54% targeted temperate organisms, 58% were restricted to a single species and 73% to benthic invertebrates. In addition, 49% of the reviewed experiments had issues with the experimental design, principally related to replication of the main test‐factors (temperature or pH), and only 11% included field assessments of processes or associated patterns. Guiding future research by this inventory of current strengths and weaknesses will expand the overall inference space of marine climate change experiments. Specifically, increased effort is required in five areas: (i) the combined effects of concurrent climate and non‐climate stressors; (ii) responses of a broader range of species, particularly from tropical and polar regions as well as primary producers, pelagic invertebrates, and fish; (iii) species interactions and responses of species assemblages, (iv) reducing pseudo‐replication in controlled experiments; and (v) increasing realism in experiments through broad‐scale observations and field experiments. Attention in these areas will improve the generality and accuracy of our understanding of climate change as a driver of biological change in marine ecosystems.     

Sequence Insertions and ITS Data Provide Congruent Information on Roccella canariensis and R. tuberculata (Arthoniales, Euascomycetes) Phylogeny

Four Roccella species, R. canariensis, R. fimbriata, R. montagnei, and R. tuberculata, were found to possess sequence insertions in up to four locations in the first half of the SSU rDNA. Insertions from one of these positions have been classified as group I introns, while the others may represent degenerative forms of group I introns or messenger RNA introns. Two of the insertion-containing taxa, R. canariensis and R. tuberculata, differ only in their dispersal strategy: R. canariensis is sexual, producing only fruiting bodies and R. tuberculata is sterile, producing only vegetative propagules, i.e., soredia. Because insertions occurred in specimens of both taxa, they were used to examine the phylogenetic relationships between and within the two species. The sequence insertions from each of the four positions were aligned and cladistically analyzed separately. Internal transcribed spacers (ITS) were additionally sequenced to study the phylogeny of all R. canariensis and R. tuberculata specimens. Three other Roccella species (R. babingtonii, R. fimbriata, and R. montagnei) and Dirina catalinariae were used as outgroups in this parsimony analysis. Sequence insertions were found to be potentially useful in phylogenetic studies, although due to the sequence dissimilarity, homology relations were difficult to establish above the species level and in some cases even within the species. The phylogenies obtained from the insertion matrices were totally consistent with the ITS data and the insertions were concluded to have been inherited. When the insertion and ITS data were combined for total evidence, R. canariensis and R. tuberculata did not form distinct lineages in the phylogenetic tree, but appeared mixed in well-supported groups containing both sorediate and fertile specimens.     

Assessment of Probable Causes of Reduced Aquatic Life in the Touchet River,Washington, USA

The Touchet River in eastern Washington State is the site of the first causal assessment in the arid Northwest for salmonids using the U.S. Environmental Protection Agency's (USEPA's) Stressor Identification process. Seven candidate causes that affect salmonid density and macroinvertebrate abundance and diversity were considered: toxics, warm water temperature, sedimentation, low dissolved oxygen, alkaline pH, reduced detritus, and reduced habitat complexity. Candidate causes were evaluated using several types of evidence of preceding causation, co-occurrence, sufficiency, and alteration along with evaluation of the consistency of that evidence and consistency with other assessments. Evidence was scored, and the body of evidence was weighed based on credibility, strength, diversity, and coherence. Warm water temperature and sedimentation were highly probable causes of altered biological condition. Low dissolved oxygen and alkaline pH were also a problem for some areas but were less severe than temperature and sediment. Water removal and reduced habitat complexity and canopy cover were not directly causal but could affect sedimentation and temperature. This case study is noteworthy for using assemblage symptomology associated with temperature, sediment, and detritus as a type of evidence and for physiographically matching reference sites for comparisons and evaluation of natural and cumulative anthropogenic stressor gradients in the absence of state biological criteria.