Preface to the Princeton Landmarks in Biology Edition vii Preface xi Symbols Used xiii 1. The Importance of Islands 3 2. Area and Number of Speicies 8 3. Further Explanations of the Area-Diversity Pattern 19 4. The Strategy of Colonization 68 5. Invasibility and the Variable Niche 94 6. Stepping Stones and Biotic Exchange 123 7. Evolutionary Changes Following Colonization 145 8. Prospect 181 Glossary 185 References 193 Index 201

The Theory of Island Biogeography

The nuclear ribosomal internal transcribed spacer (ITS) region is the formal fungal barcode and in most cases the marker of choice for the exploration of fungal diversity in environmental samples. Two problems are particularly acute in the pursuit of satisfactory taxonomic assignment of newly generated ITS sequences: (i) the lack of an inclusive, reliable public reference data set and (ii) the lack of means to refer to fungal species, for which no Latin name is available in a standardized stable way. Here, we report on progress in these regards through further development of the UNITE database (http://unite.ut.ee) for molecular identification of fungi. All fungal species represented by at least two ITS sequences in the international nucleotide sequence databases are now given a unique, stable name of the accession number type (e.g. Hymenoscyphus pseudoalbidus|GU586904|SH133781.05FU), and their taxonomic and ecological annotations were corrected as far as possible through a distributed, third-party annotation effort. We introduce the term ‘species hypothesis’ (SH) for the taxa discovered in clustering on different similarity thresholds (97–99%). An automatically or manually designated sequence is chosen to represent each such SH. These reference sequences are released (http://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and in the QIIME pipeline. The system and the data will be updated automatically as the number of public fungal ITS sequences grows. We invite everybody in the position to improve the annotation or metadata associated with their particular fungal lineages of expertise to do so through the new Web-based sequence management system in UNITE.

http://web.stanford.edu/~kpeay/papers/Koljalg_2013_MEC.pdf

Towards a unified paradigm for sequence-based identification of fungi

Crop pathogens and pests reduce the yield and quality of agricultural production. They cause substantial economic losses and reduce food security at household, national and global levels. Quantitative, standardized information on crop losses is difficult to compile and compare across crops, agroecosystems and regions. Here, we report on an expert-based assessment of crop health, and provide numerical estimates of yield losses on an individual pathogen and pest basis for five major crops globally and in food security hotspots. Our results document losses associated with 137 pathogens and pests associated with wheat, rice, maize, potato and soybean worldwide. Our yield loss (range) estimates at a global level and per hotspot for wheat (21.5% (10.1–28.1%)), rice (30.0% (24.6–40.9%)), maize (22.5% (19.5–41.1%)), potato (17.2% (8.1–21.0%)) and soybean (21.4% (11.0–32.4%)) suggest that the highest losses are associated with food-deficit regions with fast-growing populations, and frequently with emerging or re-emerging pests and diseases. Our assessment highlights differences in impacts among crop pathogens and pests and among food security hotspots. This analysis contributes critical information to prioritize crop health management to improve the sustainability of agroecosystems in delivering services to societies. An expert elicitation survey estimates yield losses for the five major food crops worldwide, suggesting that the highest losses are associated with food-deficit regions with fast-growing populations and frequently with emerging or re-emerging pests and diseases.

The global burden of pathogens and pests on major food crops.

Many studies have described the effects of urbanization on species richness. These studies indicate that urbanization can increase or decrease species richness, depending on several variables. Some of these variables include: taxonomic group, spatial scale of analysis, and intensity of urbanization. Recent reviews of birds (the most-studied group) indicate that species richness decreases with increasing urbanization in most cases but produces no change or even increases richness in some studies. Here I expand beyond the bird studies by reviewing 105 studies on the effects of urbanization on the species richness of non-avian species: mammals, reptiles, amphibians, invertebrates and plants. For all groups, species richness tends to be reduced in areas with extreme urbanization (i.e., central urban core areas). However, the effects of moderate levels of urbanization (i.e., suburban areas) vary significantly among groups. Most of the plant studies (about 65%) indicate increasing species richness with moderate urbanization whereas only a minority of invertebrate studies (about 30%) and a very small minority of non-avian vertebrate studies (about 12%) show increasing species richness. Possible explanations for these results are discussed, including the importance of nonnative species importation, spatial heterogeneity, intermediate disturbance and scale as major factors influencing species richness.

Effects of urbanization on species richness: A review of plants and animals

Re-Thinking Science: Knowledge and the Public in an Age of Uncertainty

Literature reviews are in great demand in most scientific fields. Their need stems from the ever-increasing output of scientific publications [1]. For example, compared to 1991, in 2008 three, eight, and forty times more papers were indexed in Web of Science on malaria, obesity, and biodiversity, respectively [2]. Given such mountains of papers, scientists cannot be expected to examine in detail every single new paper relevant to their interests [3]. Thus, it is both advantageous and necessary to rely on regular summaries of the recent literature. Although recognition for scientists mainly comes from primary research, timely literature reviews can lead to new synthetic insights and are often widely read [4]. For such summaries to be useful, however, they need to be compiled in a professional way [5].

When starting from scratch, reviewing the literature can require a titanic amount of work. That is why researchers who have spent their career working on a certain research issue are in a perfect position to review that literature. Some graduate schools are now offering courses in reviewing the literature, given that most research students start their project by producing an overview of what has already been done on their research issue [6]. However, it is likely that most scientists have not thought in detail about how to approach and carry out a literature review.

Reviewing the literature requires the ability to juggle multiple tasks, from finding and evaluating relevant material to synthesising information from various sources, from critical thinking to paraphrasing, evaluating, and citation skills [7]. In this contribution, I share ten simple rules I learned working on about 25 literature reviews as a PhD and postdoctoral student. Ideas and insights also come from discussions with coauthors and colleagues, as well as feedback from reviewers and editors.

/pdf/ten-simple-rules-for-writing-a-literature-review-1884xf0xfw.pdf

Ten Simple Rules for Writing a Literature Review

European ash (Fraxinus excelsior) dieback - a conservation biology challenge.

Summary
The ascomycete Hymenoscyphus pseudoalbidus (anamorph Chalara fraxinea) causes a lethal disease known as ash dieback on Fraxinus excelsior and Fraxinus angustifolia in Europe. The pathogen was probably introduced from East Asia and the disease emerged in Poland in the early 1990s; the subsequent epidemic is spreading to the entire native distribution range of the host trees. This pathogen profile represents a comprehensive review of the state of research from the discovery of the pathogen and points out knowledge gaps and research needs.

Taxonomy
Members of the genus Hymenoscyphus (Helotiales, Leotiomycetidae, Leotiomycetes, Ascomycota) are small discomycetes which form their ascomata on dead plant material. A phylogeny based on the internal transcribed spacers (ITSs) of the rDNA indicated the avirulent Hymenoscyphus albidus, a species native to Europe, as the closest relative of H. pseudoalbidus.

Symptoms
Hymenoscyphus pseudoalbidus causes necrotic lesions on leaves, twigs and stems, eventually leading to wilting and dieback of girdled shoots. Bark lesions are characterized by a typical dark- to cinnamon-brown discoloration.

Life cycle
Hymenoscyphus pseudoalbidus is heterothallic and reproduces sexually on ash petioles in the litter once a year. Ascospores are wind dispersed and infect ash leaves during the summer. The asexual spores only serve as spermatia.

Tools and techniques
The most important techniques for fungal handling, such as detection, isolation, culturing, storage, crossing and ascocarp production, are briefly described.

Management
Once the disease is established, management is hardly possible. The occurrence of a small fraction of partially tolerant trees constitutes hope for resistance breeding in the future. Healthy-looking trees should be preserved.

/pdf/hymenoscyphus-pseudoalbidus-the-causal-agent-of-european-ash-578zkxa050.pdf

Hymenoscyphus pseudoalbidus, the causal agent of European ash dieback

Wood-decaying fungi are essential for the functioning of forest ecosystems. They provide habitat for many other organisms and enable the regeneration of forests throughout the world. Since wood decomposition is a decisive process in nutrient recycling, soil formation and the carbon budget of forest ecosystems, it is receiving increasing attention from forest ecologists, pathologists and managers. Research has focussed on the factors driving the species-richness of wood-decomposing organisms and is moving on to analyse the effects of this species-richness on ecosystem functioning. Coarse woody debris (CWD) and its associated wood-decaying organisms have been drastically reduced in abundance and diversity by forestry and so these features often have potential as conservation indicators. Protective measures at a landscape level are needed for threatened wood-inhabiting fungi. These include restricting salvage operations in windthrow stands, actively encouraging the accumulation of deadwood in forests, and facilitating decay in standing trees by inoculating them with fungi. Here, we aim to collect and summarize recently produced work on deadwood ecology, pointing out research gaps and perspectives.

/pdf/wood-decaying-fungi-in-the-forest-conservation-needs-and-26bgrg787r.pdf

Wood-decaying fungi in the forest: conservation needs and management options

There has been a remarkable scientific output on the topic of how climate change is likely to affect plant diseases. This overview addresses the need for review of this burgeoning literature by summarizing opinions of previous reviews and trends in recent studies ontheimpactsofclimatechangeonplant health.Sudden Oak Death is used as an introductory case study: Cali- fornian forests could become even more susceptible to this emerging plant disease, if spring precipitations will be accompanied by warmer temperatures, although climate shifts may also affect the current synchronic- ity between host cambium activity and pathogen colonization rate. A summary of observed and pre- dicted climate changes, as well as of direct effects of climate change on pathosystems, is provided. Predic- tion and management of climate change effects on plant health are complicated by indirect effects and the interactions with global change drivers. Uncertain- ty in models of plant disease development under climate change calls for a diversity of management strategies, from more participatory approaches to in- terdisciplinary science. Involvement of stakeholders and scientists from outside plant pathology shows the importance of trade-offs, for example in the land-sharing vs. sparing debate. Further research is needed on climate change and plant health in moun- tain, boreal, Mediterranean and tropical regions, with multiple climate change factors and scenarios (includ- ing our responses to it, e.g. the assisted migration of plants), in relation to endophytes, viruses and mycor- rhiza, using long-term and large-scale datasets and considering various plant disease control methods.

/pdf/impacts-of-climate-change-on-plant-diseases-opinions-and-4r1e54tb2f.pdf

Impacts of climate change on plant diseases—opinions and trends

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