Conundrums of competitive ability in plants: what to measure?

A survey of recent literature indicates that competitive ability in plants has been measured, in most studies, only in terms of the relative intensity of size suppression experienced by competitors within one growing season. Far fewer studies have recorded relative success in terms of survival and even fewer studies have recorded fecundity under competition. Differences in size suppression are usually assumed to reflect differences in relative abilities to deny resources to competitors. However, most previous studies have failed to control or account for other sources of variation in the size suppression that plants experience under competition, i.e. variation between mixtures in the resource supply/demand ratio (approach to carrying capacity), or variation in the degree of niche overlap between competitors, or variation in the intensity of concurrent facilitative interactions between competitors. For future studies, much greater caution is required in recognizing these inherent limitations of traditional measures of competitive ability and, hence, guarding against unfounded conclusions or predictions about potential for competitive success that are based on these measures. There is also a significant challenge for future studies to adopt empirical approaches for minimizing these limitations. Some initial recommendations are considered here based on an emerging view of competitive ability measured in terms of traits associated with all three conventional components of Darwinian fitness, i.e. not just growth (plant size) but also survival and fecundity allocation (offspring production per unit plant size per unit time). According to this model, differences in competitive ability imply differences in the ability, despite intense competition (i.e. low resource supply/demand ratio), to recruit offspring into the next generation and thereby limit offspring recruitment by other plants. The important traits of competitive ability, therefore, are not only those that allow a plant to deny resources to competitors, suppress their sizes and hence, maximize the plant's own size, but also those traits that allow the plant to withstand suppression from competition enough to persist, both as an individual (through survival) and across generations (through descendants).     

Access and benefit-sharing: what indicators to measure ‘success’?

We examine challenges with measuring ‘success’ in access and benefit-sharing (ABS) of biological resources. We note a lack of indicators and draw on Pacific patent landscaping, ABS case studies, and research permit figures to highlight that ABS systems are functioning somewhat, although they are often not meeting expectations.     

Can we detect oceanic biodiversity hotspots from space?

Understanding the variability of marine biodiversity is a central issue in microbiology. Current observational programs are based on in situ studies, but their implementation at the global scale is particularly challenging, owing to the ocean extent, its temporal variability and the heterogeneity of the data sources on which compilations are built. Here, we explore the possibility of identifying phytoplanktonic biodiversity hotspots from satellite. We define a Shannon entropy index based on patchiness in ocean color bio-optical anomalies. This index provides a high resolution (1 degree) global coverage. It shows a relation to temperature and mid-latitude maxima in accordance with those previously evidenced in microbiological biodiversity model and observational studies. Regional maxima are in remarkable agreement with several known biodiversity hotspots for plankton organisms and even for higher levels of the marine trophic chain, as well as with some in situ planktonic biodiversity estimates (from Atlantic Meridional Transect cruise). These results encourage to explore marine biodiversity with a coordinated effort of the molecular, ecological and remote sensing communities.     

Cryopreservation of threatened native Australian species—what have we learned and where to from here?

Cryogenic storage techniques have been developed and adopted for more than 100 (mainly agricultural) plant species worldwide, and within Australia, at least 30 critically endangered plants have been stored long term using cryogenic approaches. Nevertheless, there are many species that are very difficult to store using current procedures, and organizations involved in plant germplasm conservation (such as botanic gardens, agricultural institutions, etc.) that utilise cryogenic storage techniques are in some respects at a crossroads in their endeavours to cheaply and effectively store a wide selection of species and genotypes for conservation and agricultural/horticultural purposes. For taxa that are not amenable to current cryogenic approaches, new ways of developing cryogenic storage techniques need to be investigated, including research into the ways in which cell membranes interact and change when cooled to cryogenic temperatures (−196°C in liquid nitrogen) in the presence of various cryoprotective agents. This review highlights the current state of cryogenic research both within Australia and internationally, provides a case study on threatened plant species and also describes several new research initiatives that aim to provide answers to why some native species are quite amenable to widely utilised cryogenic approaches whilst others are currently non-responsive. New approaches aim to integrate laboratory and membrane modelling paradigms to provide guidelines for the development of new cryopreservation protocols and to assess the robustness of theoretical models in predicting optimum cryogenic conditions.     

Inbreeding and relatedness coefficients: what do they measure?

This paper reviews and discusses what is known about the relationship between identity in state, allele frequency, inbreeding coefficients, and identity by descent in various uses of these terms. Generic definitions of inbreeding coefficients are given, as ratios of differences of probabilities of identity in state. Then some of their properties are derived from an assumption in terms of differences between distributions of coalescence times of different genes. These inbreeding coefficients give an approximate measurement of how much higher the probability of recent coalescence is for some pair of genes relative to another pair. Such a measure is in general not equivalent to identity by descent; rather, it approximates a ratio of differences of probabilities of identity by descent. These results are contrasted with some other formulas relating identity, allele frequency, and inbreeding coefficients. Additional assumptions are necessary to obtain most of them, and some of these assumptions are not always correct, for example when there is localized dispersal. Therefore, definitions based on such formulas are not always well-formulated. By contrast, the generic definitions are both well-formulated and more broadly applicable.     

How do ecologists select and use indicator species to monitor ecological change? Insights from 14 years of publication in Ecological Indicators

Indicator species (IS) are used to monitor environmental changes, assess the efficacy of management, and provide warning signals for impending ecological shifts. Though widely adopted in recent years by ecologists, conservation biologists, and environmental practitioners, the use of IS has been criticized for several reasons, notably the lack of justification behind the choice of any given indicator. In this review, we assess how ecologists have selected, used, and evaluated the performance of the indicator species. We reviewed all articles published in Ecological Indicators (EI) between January 2001 and December 2014, focusing on the number of indicators used (one or more); common taxa employed; terminology, application, and rationale behind selection criteria; and performance assessment methods. Over the last 14 years, 1914 scientific papers were published in EI, describing studies conducted in 53 countries on six continents; of these, 817 (43%) used biological organisms as indicators. Terms used to describe organisms in IS research included “ecological index”, “environmental index”, “indicator species”, “bioindicator”, and “biomonitor,” but these and other terms often were not clearly defined. Twenty percent of IS publications used only a single species as an indicator; the remainder used groups of species as indicators. Nearly 50% of the taxa used as indicators were animals, 70% of which were invertebrates. The most common applications behind the use of IS were to: monitor ecosystem or environmental health and integrity (42%); assess habitat restoration (18%); and assess effects of pollution and contamination (18%). Indicators were chosen most frequently based on previously cited research (40%), local abundance (5%), ecological significance and/or conservation status (13%), or a combination of two or more of these reasons (25%). Surprisingly, 17% of the reviewed papers cited no clear justification for their choice of indicator. The vast majority (99%) of publications used statistical methods to assess the performance of the selected indicators. This review not only improves our understanding of the current uses and applications of IS, but will also inform practitioners about how to better select and evaluate ecological indicators when conducting future IS research.     

Overyielding and species diversity: what should we expect?

Recent empirical studies have found evidence of increased biomass production ('overyielding') in species mixtures relative to monoculture, but the interpretation of these results remains controversial, in part, because of the lack of a theoretical expectation. Here, we examined the expected frequency and stability of overyielding species mixtures using Lotka-Volterra models of species dynamics in two- and four-species systems in conjunction with community, population, and specific rate of biomass production (SRP) definitions of overyielding. Overyielding plant mixtures represented > 55% of potential species assemblages under community definitions and approximately 100% of species were either overyielding or underyielding under the population definition. Our species simulations approached their equilibria in 1-2 yr, supporting the relevancy of an equilibrial analysis. The range of parameter space that we explored produced realistic values of plot biomass, supporting their biological relevance. We show that overyielding is expected to be common under community definitions and population definitions. Overyielding, under community or population definitions, does not imply an actual increase in the specific rate of biomass production. In addition, assemblages of overyielding and underyielding species under all three definitions can be stable over time with underyielding species persisting in the presence of overyielding species.     

Species concepts and floras: what are species for?

In 1992, in a special paper in the American Journal of Botany, Ernst Mayr attempted to ‘prove’ the biological species concept (BSC) worked as well in plants as it did in animals by analyzing the flora of the Concord region of northern Massachusetts. He concluded that there were minimal difficulties when applying the BSC for the plants of this particular area, and concluded that botanists were misguided in not accepting the BSC. He suggested that what he called ‘typological’ thinking was prevalent in the taxonomic community, and that this was a factor in botanical resistance to the BSC. Typology, as defined by Mayr in his 1992 foray into botany, is to a certain extent a straw‐man and, by the late 20th Century, no longer a way of thinking in widespread use in the taxonomic community in any organismal group. Here, I examine his analysis in the light of current interest in plant diversity. Species can be characterized as hypotheses about the distribution of variation in nature, subject to test with new data of many kinds. Species concepts like the BSC, although of interest philosophically and to researchers looking at mechanisms of speciation, may actually get in the way of achieving a baseline understanding of the diversity of life on Earth. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 17–25.     

Restoration of a Danube floodplain forest: what happens to species richness of terrestrial beetles?

Along the upper Danube, between river kilometer 2,472 and 2,464 (Bavaria, Germany), a managed hardwood forest was reconnected to the river via a newly carved floodplain channel. We report the stepwise alteration of the diversity of terrestrial beetles for six successive years from 2007 to 2012. In a 2‐year preliminary period (2007–2008), we recorded the baseline stage before the technical measures were implemented (2009–2010) and the onset of restoration occurred (2011–2012) with a continuous water flow in the new channel and seven flooding events. Each sample plot was equipped with a pitfall trap, an emergence photo‐eclector, an arboreal photo‐eclector, and a flight interception trap in breast height and in the canopy, respectively. The beetle communities act as an indicator to detect possible disturbance events when a riparian hardwood forest is stepwise transformed to become a new floodplain ecosystem. Within the 6‐year study period, we trapped 62,107 individual beetles, representing 85 families, 544 genera, and 1,191 species. Compared to the baseline stage, the abundance and the number of species decreased, including rare and red list species. On functional level, the species decline was particularly pronounced for zoophagous and mycetophagous species. Finally, we suppose that the 2‐year period since the launch of the new channel is too short for the establishment of a beetle community adjusted to the terrestrial part of the developing new floodplain forest.     

Conserving what,where and how? Cost-efficient measures to conserve biodiversity in Denmark

Biodiversity conservation efforts in Europe have traditionally focused on farmland and open nature areas such as grasslands, heathlands and meadows, while little attention has been devoted to conservation actions in forest. Using detailed information on the geographical distribution of about 900 terrestrial species in Denmark we apply systematic conservation planning techniques to identify how to protect biodiversity at the lowest cost to society. The results suggest that conservation actions in forest should be given a higher priority. Thus, three to four times the number of forest species are protected per million € compared with species living in open land natural areas. Furthermore, a gap analysis finds the current designation of Natura 2000 and other protected areas is skewed toward open land natural areas, and insufficient to meet the conservation targets on forest species.     

Threatened and endemic species: are they good indicators of patterns of biodiversity on a national scale?

Endemic and/or threatened species are often targeted to set conservation priorities. It is tempting to assume that a reserve network focusing on these species will be an effective umbrella for overall species richness of a country. For South Africa and Lesotho we tested whether complementary networks selected for threatened and/or endemic bird species satisfactorily represent all bird species, both in terms of capturing areas where other species are present or areas where they are more abundant (and, presumably, more viable). We found that areas selected for threatened and endemic species perform considerably better than areas selected at random. However, they do not guarantee the representation of overall bird species diversity, particularly not in peak abundance locations. Although nationally threatened and endemic species are important conservation targets, our results indicate that reserve networks focusing solely on these species may not be sufficient to preserve overall species diversity in a country.     

Dispersal to or from an African biodiversity hotspot?

Biodiversity hotspots are centres of endemism and thus contain many range-restricted species. In addition, within these hotspots occur widespread species that might have originated within a hotspot before dispersing to neighbouring or distant regions. We test this hypothesis with a phylogeographic analysis of a miniature leaf litter frog, Arthroleptis xenodactyloides , that has a large distribution throughout the Eastern Arc biodiversity hotspot and other regions in East Africa. Maximum-likelihood and Bayesian estimates of the mitochondrial gene phylogeny are used as a proxy for understanding the evolutionary history of diversification and the historical relationships between populations. The north–south range of this species extends for approximately 1900 km; our sampling covers approximately 85% of this range. Using phylogenetic comparative methods, we estimate the region of origin and direction of dispersal within A. xenodactyloides . We compare contrasting hypotheses of latitudinal range expansion using bayes factors. The ancestral region of origin of A. xenodactyloides is reconstructed as having occurred within the Eastern Arc before dispersing southwards into the southern Rift Mountains, probably in the Pleistocene. The phylogeographic structure within this leaf litter frog is surprisingly similar to that of forest birds, revealing that similar geographic features might have had a driving role in diversification of these very dissimilar taxa. Latitudinal expansion occurred early in the evolutionary history of A. xenodactyloides , which may indicate that physiological adaptation facilitated its wide geographic distribution.     

Genetic epidemiology of rheumatoid arthritis: what to expect from Latin America?

Rheumatoid arthritis is a chronic and systemic autoimmune disease characterized by inflammation and destruction of the synovial joints. It affects approximately 0.5% of the Latin-American population and is three times more common in women than in men. Evidence of familial aggregation (lambdas=2-17) was the first indication of a genetic susceptibility to disease. As in other autoimmune diseases, it has a complex genetic basis. Results from whole-genome scans indicate that the HLA region contains a significant and consistent set of linked loci. However, HLA accounts for only one-third of the genetic susceptibility of disease, indicating that non-HLA genes are also involved in the disease susceptibility. In Latin-America, association with HLA-DRB1*0404 and TNF -308A alleles has been uniformly established; however, many other candidate genes remain to be studied. The identification of genetic factors conferring susceptibility to rheumatoid arthritis will contribute to the knowledge of the pathogenic mechanisms, ability to predict its occurrence, the development of diagnostic tools, prognosis, and treatment. The genetic epidemiology of rheumatoid arthritis is herein reviewed; a set of recommendations is provided for the design, analysis and interpretation of genetic association studies in the context of Latin-American populations.     

Antioxidant activity: what do we measure?

Inhibition of oxidation of 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) by free radicals generated by decomposition of 2,2'-azobis(2-amidopropane) (ABAP) by antioxidants and biological material was studied. A correlation was found between the ability of various substances to delay the onset of ABTS oxidation and their rapid reduction of the ABTS+* cation radical, and between the ability to reduce the maximal rate of ABTS oxidation and slow reduction of ABTS+*. The length of the lag period of ABTS oxidation was found to be independent of ABTS concentration. Similar decrease of peroxynitrite-induced ABTS+* formation by antioxidants was observed when the antioxidants were added before and after peroxynitrite. All these findings indicate that the main effect of antioxidants in this system is reduction of ABTS+* and not prevention of its formation. Reduction of oxidation products rather than inhibition of their formation may be the predominant mode of action of antioxidants in various assays of antioxidant activity.     

New food sources,conservation of biodiversity and sustainable development: can unconventional animal species contribute to feeding the world?

There is increasing interest in the potential of animal species that do not currently fall within the scope of conventional livestock farming to supplement the production of animal protein for human consumption. This paper provides an overview of the current situation and the conditions the led to it, and offers an analysis of the future of wildlife usage within the general framework of sustainable development.     

Can species data only be appropriately used to conserve biodiversity?

Despite widely acknowledged handicaps of the species approach to identifying priority conservation areas, many workers continue to use these flawed techniques as the backbone of their analyses. Species-based approaches address only a small part of biological diversity by ignoring different levels of organisation as well as the functional linkages among these levels. These data are often biased and incomplete and are often used in preference to data dealing with higher biological levels of organisation though the latter may be readily available. Within the framework of Noss's [(1990) Conservation Biology 4: 355–364] hierarchical definition of biodiversity (and Scott etal. [(1993) Wildlife Monographs 123: 1–31] gap analysis), we propose a top-down model dealing with broad organisational levels first, and finer-scale species distributions last. Note that we do not discard the latter approach, but merely argue for its use at a stage when, in our opinion, it adds most to the value of the prioritisation exercise. The model is flexible so that additional information, particularly those related to threats to biological diversity, can be added when they are available.     

Control of nucleosome movement: To space or not to space nucleosomes?

A key feature of ATP-dependent chromatin remodeling complexes is how they control the ability of the complex to translocate along DNA within the context of a nucleosome. Although these complexes generally initiate DNA translocation near the dyad axis of the nucleosome, the progression and eventual termination is regulated in quite distinct ways. The best studies examples of these are the ISWI type which has strong extranucleosomal DNA dependent activity or the SWI/SNF type which has no linker DNA requirement. Recent data provide more insights into the mechanism of regulation of DNA translocation by the ISWI type complexes and how the structure of the ISWI-nucleosome complex changes during chromatin remodeling.     

Excitonic connectivity between photosystem II units: what is it, and how to measure it?

In photosynthetic organisms, light energy is absorbed by a complex network of chromophores embedded in light-harvesting antenna complexes. In photosystem II (PSII), the excitation energy from the antenna is transferred very efficiently to an active reaction center (RC) (i.e., with oxidized primary quinone acceptor Q _A), where the photochemistry begins, leading to O₂ evolution, and reduction of plastoquinones. A very small part of the excitation energy is dissipated as fluorescence and heat. Measurements on chlorophyll (Chl) fluorescence and oxygen have shown that a nonlinear (hyperbolic) relationship exists between the fluorescence yield (Φ _F ) (or the oxygen emission yield, $ \Phi _{{{\text{O}}_{2} }} $ ) and the fraction of closed PSII RCs (i.e., with reduced Q _A). This nonlinearity is assumed to be related to the transfer of the excitation energy from a closed PSII RC to an open (active) PSII RC, a process called PSII excitonic connectivity by Joliot and Joliot (CR Acad Sci Paris 258: 4622–4625, 1964). Different theoretical approaches of the PSII excitonic connectivity, and experimental methods used to measure it, are discussed in this review. In addition, we present alternative explanations of the observed sigmoidicity of the fluorescence induction and oxygen evolution curves.     

Nitrogen deposition and reduction of terrestrial biodiversity:Evidence from temperate grasslands

Biodiversity is thought to be essential for ecosystem stability, function and long-term sustainability. Since nitrogen is the limiting nutrient for plant growth in many terrestrial ecosystems, reactive nitrogen has the potential to reduce the diversity of terrestrial vegetation and associated biota through favouring species adapted to quickly exploiting available nutrients. Although the potential has long been recognised, only recently has enough evidence come together to show beyond reasonable doubt that these changes are already occurring. Linked together, experimental, regional/empirical, and time-series research provide a powerful argument that enhanced deposition of reactive nitrogen across Great Britain, and potentially the rest of Europe, has resulted in a significant and ongoing decline in grassland species richness and diversity.