Preface

Summary The number of published meta‐analyses in plant ecology has increased greatly over the last two decades. Meta‐analysis has made a significant contribution to the field, allowing review of evidence for various ecological hypotheses and theories, estimation of effects of major environmental drivers (climate change, habitat fragmentation, invasive species, air pollution), assessment of management and conservation strategies, and comparison of effects across different temporal and spatial scales, taxa and ecosystems, as well as research gap identification. We identified 322 meta‐analyses published in the field of plant ecology between 1996 and 2013 in 95 different journals and assessed their methodological and reporting quality according to standard criteria. Despite significant recent developments in the methodology of meta‐analysis, the quality of published meta‐analyses was uneven and showed little improvement over time. We found many cases of imprecise and inaccurate usage of the term ‘meta‐analysis’ in plant ecology, particularly confusion between meta‐analysis and vote counting and incorrect application of statistical techniques designed for primary studies to meta‐analytical data, without recognition of the violation of statistical assumptions of the analyses. Methodological issues for meta‐analyses in plant ecology include incomplete reporting of search strategy used to retrieve primary studies, failure to test for possible publication bias and to conduct sensitivity analysis to test the robustness of the results, as well as lack of availability of the data set used for the analyses. The use of meta‐analysis is particularly common in community ecology, ecophysiology and ecosystem ecology, but meta‐analyses in ecophysiology are more likely not to meet standard quality criteria than papers in other subdisciplines. Fewer meta‐analyses have been conducted in plant population ecology. Synthesis. Over the past two decades, plant ecologists have embraced meta‐analysis as a statistical tool to combine results across studies, and much has been learned as a result. However, as the popularity and usage of meta‐analysis in the field of plant ecology has grown, establishment of quality standards, as has been done in other disciplines, becomes increasingly important. In order to improve the quality of future meta‐analyses in plant ecology, we suggest adoption of a checklist of quality criteria for meta‐analysis for use by research synthesists, peer reviewers and journal editors.

<i>Journal of Ecology</i> News

Over the last decade, the field of plant ecology has significantly developed and expanded, especially in research concerning the herb layer and ground vegetation of forests. This revised second edition accounts for that growth, presenting research that approaches the ecology of the herb layer of forests from a variety of disciplines and perspectives. The book synthesizes the research of top ecologists and biologists on herbaceous layer structure, composition, and dynamics of a variety of forest ecosystem types in eastern North America. The 2003 first edition of this book was praised for containing the most extensive listing of herb-layer literature in existence. This second edition brings this material up to date, revised to include current research and data. The book incorporates quantitative data to support analyses that was previously unavailable during the publication of the first edition. Also featured are six entirely new chapters, focused on the response of the herbaceous layer to a wide variety of natural and anthropogenic disturbances.

This essay describes the career and professional development of the author in the field of plant ecology between the 1970s and early 2000s. Early experiences of under- and postgraduate training reveal the similarity between the late 20th century, and the present-day, in the struggle to obtain a career and stable employment. I describe the booming development of conservation ecology as applied in production landscapes together with the collapse of support for this work two decades later. However, continuity in my research has been provided by the enduring themes of plant functional types and grassland conservation. The experience of second wave feminism and its translation into gender issues in the workplace is also considered. Finally, tips are provided on professional development, collaborations, research strategies, professional practice, writing and communication.

Considering the rapid advancement of the biomedical sciences, the molecular and cellular biology of most host–parasite interactions remains still largely enigmatic. Some of the best understood parasites are those that cause malaria, one of the leading causes of death from infectious diseases throughout human history and still today. This special issue on malaria testifies how much progress has been made, but also shows how much more remains to be discovered. Not only do we lack a proven rationale for a cheap vaccine, but there are still many open questions about the most basic processes of malaria parasite biology and how the parasite interacts with its hosts. This leaves plenty of scope for new and fundamental discoveries that would gain immensely from attracting scientists from other fields and funding agencies alike. Excerpt from the comic ‘Malaria – the battle against a microscopic killer’. Comic written and created by Jamie Hall and Edward Ross, cover designed by Luke Pearson and colouring by Tom Humberstone. This comic is funded by the European Commission FP7 Network of Excellence EVIMalaR © 2012. This special issue is thus also a tribute to the many researchers that have not only worked hard and openly exchanged their ideas and findings on sometimes very competitive issues but also to those that provided for the future by inspiring and training the next generation of researchers. Within these pages you will find a showcase of international work with contributions from colleagues in North America, Europe, Asia and Australia but an ominous absence of contributions from Africa, where malaria causes most deaths. This single fact highlights the ongoing and urgent need for stronger research capacity building right where it is most needed. There are myriad interactions between the malaria parasite and its different host cells and tissues and no special issue would be able to even attempt to portrait them all. Nevertheless, the selection of review and primary research presented here give a good overview of the divergence of research topics in malaria research and hence the scope of the problem. This research has always benefited from the use of model organisms from the discovery of parasite transmission by Ronald Ross using birds and the discovery of the liver stages using monkeys as well as the use of mice for early vaccine studies in the late 1960s. Therefore, a timely review examines the success and promise of humanized rodent models for the study of malaria infection (Kaushansky et al.). Similar to animal models the cultivation of a parasite in cell culture is necessary to advance our understanding of its molecular biology. This is highlighted by another review focusing on how Plasmodium knowlesi, a parasite mainly infecting monkeys but also deadly for humans, can be cultivated (Grüring et al.). To understand the pathology of parasite host interaction the first contact is often of great importance. This is mediated by proteins on the parasite surface that can interact with proteins on the host cell. How these specific proteins help to attach parasites to their host cells is thus the topic of a third review (Malpede and Tolia). Malaria parasites are ancient organisms and thus feature organelles that seem alien to students of metazoan biology. To this end a fourth review (Harding and Meissner) describes one such essential organelle that defines malaria parasites and related organisms. The primary research reported in this special issue touches almost all parts of the malaria parasite life cycle. Starting from the bite of the mosquito, which delivers Plasmodium sporozoites into the skin (Carey et al.), the development in the liver (Austin et al.) to the invasion of merozoites into red blood cells (Knüpfer et al.; Yap et al.), the trafficking within and adherence of the infected red blood cells to the vasculature (Brugat et al., Esser et al. and Siau et al.), the escape of the parasites from the red blood cell (Wirth et al.), the penetration of the mosquito gut wall by ookinetes (Kan et al.) and the conversion of these into cysts where new sporozoites are formed (Andreadaki et al.).

Editorial and Retrospective 2008

Changes in grassland phenology and growth rate, rather than diversity, drive biomass production after fire

Using a mixed culture replacement method, different plant species are planted with different densities per unit area. The benefits of using this method are evident; however, phytotoxic/competitive effects of these different plant species on each other are rarely studied, especially for cotton. Allelopathy is a biological phenomenon that can affect many aspects of plant ecology. A pot experiment was conducted to determine the individual and/or interactive effects of cotton, sesame, and green gram on each other. Sesame, green gram, and cotton were sown in a replacement series in three different combinations: Sesame–cotton (3–0, 2–1, 1–2, 0–3); sesame–green gram (3–0, 2–1, 1–2, 0–3); and cotton–green gram (3–0, 2–1, 1–2, 0–3). The experiment was conducted using a completely randomized design with four replications; results revealed that inclusion of a legume crop (i.e., green gram) significantly improved cotton shoot and root growth and yield, but sowing of sesame with cotton considerably decreased cotton plant performance as compared to green gram. Similarly, sesame plant height was improved by increasing the number of cotton and green gram plants per pot. The effects of sesame and cotton were deleterious for green gram. It was concluded that high‐stature crops (such as the main crop) can be grown with short‐stature leguminous crops as the companion crop.

In marine environment, non-indigenous species (NIS) can alter natural habitats and cause biodiversity loss with important consequences for ecosystems and socio-economic activities. With more than 1000 NIS introduced over the last century, the Mediterranean Sea is one of the most threatened regions worldwide, requiring an early identification of newly entered alien species for a proper environmental management. Here, we carried out environmental-DNA (eDNA) metabarcoding analyses, using multiple molecular markers (i.e., 18S rRNA, COI, and rbcL) and different genetic databases (i.e., NCBI, PR2, SILVA, MIDORI2, MGZDB, and BOLD), on seawater and sediment samples collected on a seasonal basis in three Mediterranean ports located in the North Adriatic, Ionian and Tyrrhenian Sea to identify marine species, and particularly NIS. The use of the multi-marker eDNA metabarcoding allowed the identification of a higher number of species compared to the morphological analyses (1484 vs. 752 species), with a minor portion of species shared by both approaches. Overall, only 4 NIS were consistently identified by both morphological and molecular approaches, whereas 27 and 17 NIS were exclusively detected by using eDNA metabarcoding and classical taxonomic analyses, respectively. The eDNA metabarcoding allowed also identifying the genetic signatures of 5 NIS never reported in the Italian waters. We conclude that eDNA metabarcoding can represent a highly sensitive tool for the early identification of NIS, but a comprehensive census of the NIS requires the combination of molecular and morphological approaches.

The nutrient absorption-transportation hypothesis: optimizing structural traits in absorptive roots.

The most spectacular progress in bryological research during the last few years was certainly made in phylogeny. Essentially molecular approaches refined our views of the evolution of bryophyte lineages. The recent developments in laboratory techniques (namely the polymerase chain reaction and automatic sequencing) and in computer tools for the fast application of sophisticated statistics provided new, concise methods to evaluate phylogenetic relationships at any level. These tools are now widely used in many disciplines and will eventually improve systematics as an integrative science of diversity. Population biology, morphogenesis, cytology, ecology, paleobotany and other fields contribute to a better understanding of evolutionary processes. Thus, research in systematics has become interdisciplinary and, consequently, it is more difficult to divide a chapter such as this into clear-cut disciplinary parts. This interdisciplinarity also leads bryologists to not only publish in their specialized periodicals but to present “their” organisms (alas, often overlooked or forgotten) in places where they will reach a larger audience.KeywordsCladistic AnalysisPeat MossEarly Land PlantPleurocarpous MossLeafy LiverwortThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

The Diverse Contributions of J. Roger Bray and Gwendolyn Struik

Cowles was professor of plant ecology at the University of Chicago when Victor Shelford brought to him the idea of forming an ecological society in 1914. Cowles convened a meeting at the AAAS meetings in December 1914 to discuss the possibility of a new society. He served as secretary and treasurer of a committee formed at that meeting to present a plan for the organization of what would become the Ecological Society of America. The other members of the committee were J. W. Harshberger, V. E. Shelford, R. H. Wolcott, Charles C. Adams, and Forrest Shreve. At the AAAS meetings in Columbus, Ohio, the committee convened a meeting on 28 December 1915. There, about 50 people enthusiastically endorsed the formation of an ecological society and the committee displayed supportive letters from another 50 potential members who could not be present in Columbus. A constitution was proposed and adopted, and the new society chose its officers for 1916. Cowles was not one of the first officers but served as the third President in 1918. His interests were in physiographic ecology, experimental ecology, forest ecology, and applied ecology. By 1916 he had conducted ecological work in 15 states across the nation, often in conjunction with summer field courses. He is best known for developing the concept of ecological succession based on studies of the Indiana sand dunes along Lake Michigan. Cowles had enormous influence on the development of ecology through his teaching at Chicago. Image courtesy of the University of Chicago. American Environmental Photographs Collection, [AEP Image Number, e.g., AEP-MIN73], Department of Special Collections, University of Chicago Library. When he became the first President of the Ecological Society of America in 1916, Shelford had recently moved from the University of Chicago to become assistant professor of zoology at the University of Illinois, Urbana, and a biologist with the Illinois State Laboratory of Natural History. He had already published on a wide range of topics, including ecological succession of beetles, fishes, and land invertebrates, ecological classification, fish migrations, physiological animal geography, animal communities, and the general principles of animal ecology. Shelford began his undergraduate studies at West Virginia University, then transferred to the University of Chicago and came under the influence of Henry Cowles. His dissertation at Chicago, completed in 1907, focused on the ecology of tiger beetles in the sand dunes. His Chicago-area studies also led to an important early book on physiological ecology, Animal Communities in Temperate America (1913). Shelford was a champion of experimental ecology, improved laboratory facilities to assist ecological studies, and promoted the preservation of natural areas. Upon moving to the University of Illinois in 1914, he insisted on construction of a new laboratory, the Vivarium, to support experimental work. Shelford worked with Cowles to recruit new members in the Midwest. Image courtesy of University of Illinois Archives. Wheeler's doctoral work was in insect embryology at Clark University, Massachusetts, after which he joined the newly created University of Chicago in 1892 as an embryology instructor. Leaving Chicago in 1899 for a faculty position at the University of Texas, Austin, his research turned toward the behavior of social insects, especially ants, a subject on which he became a leading authority. After Texas, five years of work as Curator at the American Museum of Natural History in New York led to his appointment at the Bussey Institution at Harvard University in 1908, where he remained for the rest of his career as professor of economic entomology. While Wheeler had in 1902 recommended that zoologists adopt the term “ethology” in preference to “oecology” to describe their interests in the study of organisms in relation to their living and nonliving environments, he nonetheless joined the new ecological society and served as its first Vice-President in 1916. At the time he was interested in ecological work in relation to geographical distribution and animal behavior. Entomology was fairly well represented in the early Society's membership and constituted the fourth largest interest group, after animal ecology, plant ecology, and forestry. Wheeler was responsible for recruiting new members in the Northeastern U.S. during the Society's organizational year (1916), but drew in colleagues interested in social insects from a much broader area. The Ecological Society's first Secretary and Treasurer, and its President in 1922, Shreve was at the time of the Society's founding a botanist at the Desert Botanical Laboratory, Tucson, Arizona, and staff member of the Department of Botanical Research, Carnegie Institution of Washington. His research involved the relation of climatic and soil conditions to the distribution of vegetation in Maryland, Jamaica, California, and Arizona. He was broadly interested in the relation of climate to vegetation throughout the U.S., and he studied factors affecting the establishment of desert perennials. Shreve, a Marylander, completed his Ph.D. at Johns Hopkins University in 1905. His early research was devoted to the study of the mountain vegetation of Jamaica, but in 1908 he joined the newly created Desert Botanical Laboratory, which was fast growing into a thriving center of botanical research—much of it devoted to ecological topics. There, his interests turned to the effects of climate on desert vegetation. Shreve also edited the laboratory's journal, Plant World, which eventually was handed over to the Ecological Society of America and evolved into the journal Ecology. Shreve was responsible for recruiting new members in the western U.S., and brought in a number of foresters, range managers, and other applied ecologists in government employ as well as university and private researchers.

Nitric Oxide and Signaling in Plants

Comparing microarrays and next-generation sequencing technologies for microbial ecology research