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.     

The mid-domain effect and species richness patterns:what have we learned so far?

If species' ranges are randomly shuffled within a bounded geographical domain free of environmental gradients, ranges overlap increasingly toward the center of the domain, creating a "mid-domain" peak of species richness. This "mid-domain effect" (MDE) has been controversial both in concept and in application. Empirical studies assess the degree to which the evolutionary, ecological, and historical processes that undeniably act on individual species and clades produce geographical patterns that resemble those produced by MDE models. MDE models that resample empirical range size frequency distributions (RSFDs) balance the risk of underestimating and overestimating the role of MDE, whereas theoretical RSFDs are generally biased toward underestimating MDE. We discuss the inclusion of nonendemic species in MDE models, rationales for setting domain limits, and the validity of one- and two-dimensional MDE models. MDE models, though null models, are not null hypotheses to be simplistically rejected or accepted. They are a means of estimating the expected effect of geometric constraints within the context of multiple causality. We call for assessment of MDE on an equal statistical footing with other candidate explanations for richness gradients. Although some critics have categorically dismissed MDE, an overview of the 21 MDE studies published to date reveals a substantial signature of MDE in natural patterns and justifies continued work.     

Candida pneumonia: What we know and what we don’t

The diagnosis of Candida pneumonia is a difficult one to make, and some experts often question whether the entity truly exists. This article assimilates the information currently available regarding Candida pulmonary infection to elucidate the presentation of the disease and the hosts in which it occurs. It also describes how to interpret the presence of Candida in respiratory secretions from both immunocompetent and immunocompromised patients. Finally, it describes how the diagnosis of Candida pneumonia can be made, which patients with suspected disease should be treated, and which antifungal agents should be used.     

When should we save the most endangered species?

At the heart of our efforts to protect threatened species, there is a controversial debate about whether to give priority to cost-effective actions or whether focusing solely on the most endangered species will ultimately lead to preservation of the greatest number of species. By framing this debate within a decision-analytic framework, we show that allocating resources solely to the most endangered species will typically not minimise the number of extinctions in the long-term, as this does not account for the risk of less endangered species going extinct in the future. It is only favoured when our planning timeframe is short or we have a long-term view and we are optimistic about future conditions. Conservation funding tends to be short-term in nature, which biases allocations to more endangered species. Our work highlights the need to consider resource allocation for biodiversity over the long-term; 'preventive conservation', rather than just short-term fire-fighting.     

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.     

Genome data: what do we learn?

Genome sequence information has continued to accumulate at a spectacular pace during the past year. Details of the sequence and gene content of human chromosome 22 were published. The sequencing and annotation of the first two Arabidopsis thaliana chromosomes was completed. The sequence of chromosome 3 from Plasmodium falciparum, the second sequenced malaria chromosome, was reported, as was that of chromosome 1 from Leishmania major. The complete genomic sequences of five microbes were reported. Approaches to using data from completely sequenced microbial genomes in phylogenetic studies are being explored, as is the application of microarrays to whole genome expression analysis.     

Statin pharmacogenomics: what have we learned, and what remains unanswered?

PURPOSE OF REVIEW: Statins are widely prescribed and are established as first-line therapy for the primary and secondary prevention of coronary heart disease. Response to treatment varies considerably from person to person; however, inherited traits (genetic variability) may play a central role in this inter-individual variation. The purpose of this review is to summarize recent progress in the research for exploring genetic determinants of clinical efficacy and safety of statin therapy. RECENT FINDINGS: In addition to 41 previous studies of 19 genes, the results of 17 pharmacogenomic studies investigating the relationship between common genetic variants and response to statin therapy in terms of lipid responses, clinical outcomes, and adverse events have been reported since January 2004 - 15 candidate genes related to pharmacodynamics and three to pharmacokinetics of statins. These reported data suggest that genetic variations influencing intestinal cholesterol absorption, cholesterol production, and lipoprotein catabolism may all play a role in modulating responsiveness, as well as genes involved in drug metabolism of statins. They also suggest that combined analysis of multiple variants in several genes, all of which have possible functional relations, is more likely to give significant results, especially when being performed with a larger number of participants. SUMMARY: Pharmacogenomic studies of statin therapy will provide a better picture as to who is most likely and least likely to benefit from treatment, which results in more individualized management of coronary artery disease.     

UV radiation: what we know and do we protect ourselves adequately?

Chronic sun exposure causes degenerative changes in the skin that are recognized as photoaging, immunosuppression and photocarcinogenesis. Sun is necessary for life, so total sun avoidance is impossible. Sun exposure during the first 15 years of life and blistering sunburns before age 20 have been linked to an increased risk of melanoma. Individuals who have outdoor lifestyles, live in sunny climates, and are lightly pigmented will experience the greatest degree of photoaging. In our study, performed four years ago, we have shown the knowledge of more than 4000 people about the effects of UV rays on the skin. The results show us that sun exposure is still exaggerated and uncontrolled due to the lack of knowledge about this topic. Encouraging photoprotection and improving the awareness of the general public about the harmful effects of too much sun exposure must be the leading preventative health strategy.     

Imaging for lung physiology: what do we wish we could measure?

The role of imaging as a tool for investigating lung physiology is growing at an accelerating pace. Looking forward, we wished to identify unresolved issues in lung physiology that might realistically be addressed by imaging methods in development or imaging approaches that could be considered. The role of imaging is framed in terms of the importance of good spatial and temporal resolution and the types of questions that could be addressed as these technical capabilities improve. Recognizing that physiology is fundamentally a quantitative science, a recurring emphasis is on the need for imaging methods that provide reliable measurements of specific physiological parameters. The topics included necessarily reflect our perspective on what are interesting questions and are not meant to be a comprehensive review. Nevertheless, we hope that this essay will be a spur to physiologists to think about how imaging could usefully be applied in their research and to physical scientists developing new imaging methods to attack challenging questions imaging could potentially answer.     

So what is a species anyway? A primatological perspective

Since Darwin's time, the question “what a species” has provoked fierce disputes and a tremendous number of publications, from short opinion papers to thick volumes. 1 The debates covered fundamental philosophical questions, such as: Do species exist at all independently of a human observer or are they just a construct of the human mind to categorize nature's organismic diversity and serve as a semantic tool in human communication about biodiversity? 2 - 4 or: Are species natural kinds (classes) or individuals that are “born” by speciation, change in course of time, and finally “die” when they go extinct or diverge into new species? 5 - 8 Also included was the problem of species as taxa (taxonomic) versus species as products of the speciation process (evolutionary). 9 More pragmatic issues arose, such as: How can we reliably delineate and delimitate species? 10 , 11 The great interest in what a species is reflects the importance of “species” as fundamental units in most fields of biology, especially evolutionary biology, ecology, and conservation. 2 , 12 - 14     

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.     

Community genetics: what have we accomplished and where should we be going?

Research in community genetics seeks to understand how the dynamic interplay between ecology and evolution shapes simple and complex communities and ecosystems. A community genetics perspective, however, may not be necessary or informative for all studies and systems. To better understand when and how intraspecific genetic variation and microevolution are important in community and ecosystem ecology, we suggest future research should focus on three areas: (i) determining the relative importance of intraspecific genetic variation compared with other ecological factors in mediating community and ecosystem properties; (ii) understanding the importance of microevolution in shaping ecological dynamics in multi-trophic communities; and (iii) deciphering the phenotypic and associated genetic mechanisms that drive community and ecosystem processes. Here, we identify key areas of research that will increase our understanding of the ecology and evolution of complex communities but that are currently missing in community genetics. We then suggest experiments designed to meet these current gaps.     

Marine phage genomics: what have we learned?

Marine phages are the most abundant and diverse form of life on the planet, and their genomes have been described as the largest untapped reservoir of genomic information. To date, however, the complete genome sequences of only 17 marine phage are known. Nevertheless, these genomes have revealed some interesting features, including the presence of photosynthetic genes in cyanophage and common patterns of genomic organization. Intriguing findings are also being made from studies of the uncultivated marine viral community genome ('metavirome'). The greatest challenge in interpreting the biology of these phages, and for making comparisons with their terrestrial counterparts, is the high proportion of unidentifiable open reading frames (approximately 60%). Future studies are likely to focus on sequencing more marine phage genomes from disparate hosts and diverse environments and on further basic studies of the biology of existing marine phages.