Orchid diversity: an evolutionary consequence of deception?

The Orchidaceae are one of the most species-rich plant families and their floral diversity and pollination biology have long intrigued evolutionary biologists. About one-third of the estimated 18,500 species are thought to be pollinated by deceit. To date, the focus has been on how such pollination evolved, how the different types of deception work, and how it is maintained, but little progress has been made in understanding its evolutionary consequences. To address this issue, we discuss here how deception affects orchid mating systems, the evolution of reproductive isolation, speciation processes and neutral genetic divergence among species. We argue that pollination by deceit is one of the keys to orchid floral and species diversity. A better understanding of its evolutionary consequences could help evolutionary biologists to unravel the reasons for the evolutionary success of orchids.     

Catching a 'hopeful monster': shepherd's purse (Capsella bursa-pastoris) as a model system to study the evolution of flower development

Capsella is a small genus within the mustard family (Brassicaceae). Its three species, however, show many evolutionary trends also observed in other Brassicaceae (including Arabidopsis) and far beyond, including transitions from a diploid, self-incompatible, obligatory outcrossing species with comparatively large and attractive flowers but a restricted distribution to a polyploid, self-compatible, predominantly selfing, invasive species with floral reductions. All these evolutionary transitions may have contributed to the fact that Capsella bursa-pastoris (shepherd's purse) has become one of the most widely distributed flowering plants on our planet. In addition, Capsella bursa-pastoris shows a phenomenon that, although rare, could be of great evolutionary importance, specifically the occurrence of a homeotic variety found in relatively stable populations in the wild. Several lines of evidence suggest that homeotic changes played a considerable role in floral evolution, but how floral homeotic varieties are established in natural populations has remained a highly controversial topic among evolutionary biologists. Due to its close relationship with the model plant Arabidopsis thaliana, numerous experimental tools are available for studying the genus Capsella, and further tools are currently being developed. Hence, Capsella provides great opportunities to investigate the evolution of flower development from molecular developmental genetics to field ecology and biogeography, and from morphological refinements to major structural transitions.     

Paradigm change in evolutionary microbiology

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn's account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn's relevance to this controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn's account may capture aspects of the pattern (or outcome) of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn's application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader.     

Molecular insights into the evolution of crop plants

The domestication and improvement of crop plants have long fascinated evolutionary biologists, geneticists, and anthropologists. In recent years, the development of increasingly powerful molecular and statistical tools has reinvigorated this now fast-paced field of research. In this paper, we provide an overview of how such tools have been applied to the study of crop evolution. We also highlight lessons that have been learned in light of a few long-standing and interrelated hypotheses concerning the origins of crop plants and the nature of the genetic changes underlying their evolution. We conclude by discussing compelling evolutionary genomic approaches that make possible the efficient and unbiased identification of genes controlling crop-related traits and provide further insight into the actual timing of selection on particular genomic regions.     

Calculating life? Duelling discourses in interdisciplinary systems biology

A high profile context in which physics and biology meet today is in the new field of systems biology. Systems biology is a fascinating subject for sociological investigation because the demands of interdisciplinary collaboration have brought epistemological issues and debates front and centre in discussions amongst systems biologists in conference settings, in publications, and in laboratory coffee rooms. One could argue that systems biologists are conducting their own philosophy of science. This paper explores the epistemic aspirations of the field by drawing on interviews with scientists working in systems biology, attendance at systems biology conferences and workshops, and visits to systems biology laboratories. It examines the discourses of systems biologists, looking at how they position their work in relation to previous types of biological inquiry, particularly molecular biology. For example, they raise the issue of reductionism to distinguish systems biology from molecular biology. This comparison with molecular biology leads to discussions about the goals and aspirations of systems biology, including epistemic commitments to quantification, rigor and predictability. Some systems biologists aspire to make biology more similar to physics and engineering by making living systems calculable, modelable and ultimately predictable-a research programme that is perhaps taken to its most extreme form in systems biology's sister discipline: synthetic biology. Other systems biologists, however, do not think that the standards of the physical sciences are the standards by which we should measure the achievements of systems biology, and doubt whether such standards will ever be applicable to 'dirty, unruly living systems'. This paper explores these epistemic tensions and reflects on their sociological dimensions and their consequences for future work in the life sciences.     

Osmolyte accumulation: can it really help increase crop yield under drought conditions?

Osmolyte accumulation (OA) is frequently cited as a key putative mechanism for increasing yields of crops subjected to drought conditions. The hypothesis is that OA results in a number of benefits that sustain cell and tissue activity under water-deficit conditions. It has been proposed as an effective tolerance mechanism for water deficits, which could be enhanced in crops by traditional plant breeding, marker-assisted selection or genetic engineering, to generate drought-tolerant crops. However, field studies examining the association between OA and crop yield have tended to show no consistent benefit. The few, often-cited, investigations with positive associations were obtained under severe water deficits with extremely low yields or conditions with special water-supply scenarios when much of the benefit is plant survival. Under conditions where water deficits threaten crop survival, yields are so low that even large fractional yield gains offer little practical benefit to growers. Indeed, the often-cited benefit of turgor maintenance in cells is likely to result in crop behaviour that is exactly opposite to what is beneficial to crops. The one clear mechanism identified in this review for beneficial yield responses to OA is in the maintenance of root development in order to reach water that may be available deeper in the soil profile.     

The isolation of nucleic acid from nematodes requires an understanding of the parasite and its cuticular structure

As parasitology increasingly becomes the domain of molecular biologists, it is important to keep in mind that a fundamental understanding of the whole parasite, its structure and behaviour can help to solve complex problems of molecular biology. Hugh Dawkins and Terence Spencer discuss the preparation of DNA from filaform larvae of Trichostrongylus colubriformis and Ostertagia circumcincta and how a detailed knowledge of the morphology and life cycle of each parasite helps in this process.     

Use of the root contact concept,an empirical leaf conductance model and pressure-volume curves in simulating crop water relations

A simulation model “DanStress” was developed for studying the integrated effects of soil, crop and climatic conditions on water relations and water use of field grown cereal crops. The root zone was separated into 0.1 m deep layers of topsoil and subsoil. For each layer the water potential at the root surface was calculated by a single root model, and the uptake of water across the root was calculated by a root contact model. Crop transpiration was calculated by Monteith's combination equation for vapour flow. Crop conductance to water vapour transfer for use in Monteith's combination equation was scaled up from an empirical stomatal conductance model used on sunlit and shaded crop surfaces of different crop layers. In the model, transpirational water loss originates from root water uptake and changes in crop water storage. Crop water capacitance, used for describing the water storage, was derived from the slope of pressure-volume (PV) curves of the leaves. PV curves were also used for deriving crop water potential, osmotic potential, and turgor pressure. The model could simulate detailed diurnal soil-crop water relations during a 23-day-drying cycle with time steps of one hour. During the grain filling period in spring barley (Hordeum distichum L.), grown in a sandy soil in the field, measured and predicted values of leaf water and osmotic potential, RWC, and leaf stomatal conductance were compared. Good agreement was obtained between measured and predicted values at different soil water deficits and climatic conditions. In the field, measured and predicted volumetric soil water contents (θ) of topsoil and subsoil layers were also compared during a drying cycle. Predicted and measured θ-values as a function of soil water deficits were similar suggesting that the root contact model approach was valid. From the investigation we concluded: (I) a model, which takes the degree of contact between root surface and soil water into account, can be used in sandy soil for calculation of root water uptake, so that the root conductance during soil water depletion only varies by the degree of contact; (II) crop conductance, used for calculation of crop transpiration, can be scaled up from an empirical single leaf stomatal conductance model controlled by the level of leaf water potential and micrometeorological conditions; (III) PV curves are usable for describing crop water status including crop water storage.     

The role of ethics in experimental marine biology and ecology

Although most countries have ethical guidelines for research involving human subjects and other sentient animals, the ethical issues associated with field research have received little attention. Most experimental marine biologists and ecologists operate without ethical guidelines or scrutiny, despite intermittent community concern about their activities. We offer suggestions on how marine biologists and ecologists can protect the future of research involving the field collection and experimental manipulation of organisms by developing mechanisms to address community concerns that such research is ethically responsible. We urge experimental marine biologists and ecologists to take pre-emptive initiatives by encouraging: (1) institutional animal ethics committees to broaden their terms of reference to include environmental ethics; (2) scientific societies to develop codes of ethics to guide the environmental research conducted by their members; (3) editorial boards of journals to require the research they publish to conform to an appropriate code of ethics, and (4) management agencies that issue permits for field research to establish an ethics committee to advise them on the ethical issues raised by specific research proposals. We conclude that the resultant administrative burden on scientists would be low but that the penalties of operating without such protection can be high.     

A practical guide for the computational selection of residues to be experimentally characterized in protein families

In recent years, numerous biocomputational tools have been designed to extract functional and evolutionary information from multiple sequence alignments (MSAs) of proteins and genes. Most biologists working actively on the characterization of proteins from a single or family perspective use the MSA analysis to retrieve valuable information about amino acid conservation and the functional role of residues in query protein(s). In MSAs, adjustment of alignment parameters is a key point to improve the quality of MSA output. However, this issue is frequently underestimated and/or misunderstood by scientists and there is no in-depth knowledge available in this field. This brief review focuses on biocomputational approaches complementary to MSA to help distinguish functional residues in protein families. These additional analyses involve issues ranging from phylogenetic to statistical, which address the detection of amino acids pivotal for protein function at any level. In recent years, a large number of tools has been designed for this very purpose. Using some of these relevant, useful tools, we have designed a practical pipeline to perform in silico studies with a view to improving the characterization of family proteins and their functional residues. This review-guide aims to present biologists a set of specially designed tools to study proteins. These tools are user-friendly as they use web servers or easy-to-handle applications. Such criteria are essential for this review as most of the biologists (experimentalists) working in this field are unfamiliar with these biocomputational analysis approaches.     

Genetic and management approaches to boost UK wheat yields by ameliorating water deficits

Faced with the challenge of increasing global food production, there is the need to exploit all approaches to increasing crop yields. A major obstacle to boosting yields of wheat (an important staple in many parts of the world) is the availability and efficient use of water, since there is increasing stress on water resources used for agriculture globally, and also in parts of the UK. Improved soil and crop management and the development of new genotypes may increase wheat yields when water is limiting. Technical and scientific issues concerning management options such as irrigation and the use of growth-promoting rhizobacteria are explored, since these may allow the more efficient use of irrigation. Fundamental understanding of how crops sense and respond to multiple abiotic stresses can help improve the effective use of irrigation water. Experiments are needed to test the hypothesis that modifying wheat root system architecture (by increasing root proliferation deep in the soil profile) will allow greater soil water extraction thereby benefiting productivity and yield stability. Furthermore, better knowledge of plant and soil interactions and how below-ground and above-ground processes communicate within the plant can help identify traits and ultimately genes (or alleles) that will define genotypes that yield better under dry conditions. Developing new genotypes will take time and, therefore, these challenges need to be addressed now.     

C4 cycles: past, present, and future research on C4 photosynthesis

In the late 1960s, a vibrant new research field was ignited by the discovery that instead of fixing CO(2) into a C(3) compound, some plants initially fix CO(2) into a four-carbon (C(4)) compound. The term C(4) photosynthesis was born. In the 20 years that followed, physiologists, biochemists, and molecular and developmental biologists grappled to understand how the C(4) photosynthetic pathway was partitioned between two morphologically distinct cell types in the leaf. By the early 1990s, much was known about C(4) biochemistry, the types of leaf anatomy that facilitated the pathway, and the patterns of gene expression that underpinned the biochemistry. However, virtually nothing was known about how the pathway was regulated. It should have been an exciting time, but many of the original researchers were approaching retirement, C(4) plants were proving recalcitrant to genetic manipulation, and whole-genome sequences were not even a dream. In combination, these factors led to reduced funding and the failure to attract young people into the field; the endgame seemed to be underway. But over the last 5 years, there has been a resurgence of interest and funding, not least because of ambitious multinational projects that aim to increase crop yields by introducing C(4) traits into C(3) plants. Combined with new technologies, this renewed interest has resulted in the development of more sophisticated approaches toward understanding how the C(4) pathway evolved, how it is regulated, and how it might be manipulated. The extent of this resurgence is manifest by the publication in 2011 of more than 650 pages of reviews on different aspects of C(4). Here, I provide an overview of our current understanding, the questions that are being addressed, and the issues that lie ahead.     

Deep Phylogeny��How a Tree Can Help Characterize Early Life on Earth

The Darwinian concept of biological evolution assumes that life on Earth shares a common ancestor. The diversification of this common ancestor through speciation events and vertical transmission of genetic material implies that the classification of life can be illustrated in a tree-like manner, commonly referred to as the Tree of Life. This article describes features of the Tree of Life, such as how the tree has been both pruned and become bushier throughout the past century as our knowledge of biology has expanded. We present current views that the classification of life may be best illustrated as a ring or even a coral with tree-like characteristics. This article also discusses how the organization of the Tree of Life offers clues about ancient life on Earth. In particular, we focus on the environmental conditions and temperature history of Precambrian life and show how chemical, biological, and geological data can converge to better understand this history.

“You know, a tree is a tree.  How many more do you need to look at?”–Ronald Reagan (Governor of California), quoted in the Sacramento Bee, opposing expansion of Redwood National Park, March 3, 1966

The following article addresses a period in life most removed from life’s origins compared with other articles in this collection. The article discusses an advanced form of life that seems to have lived on the order of 3.5–4.0 billion years ago, around the time when life as we know it began to diversify in a Darwinian sense. The life from this geological period is located deep within an illustrated taxonomic tree of life. The hope is that by understanding how early life evolved, we can better understand how life originated. In this sense, the article attempts to travel backwards in time, starting from modern organisms, to understand life’s origin.The Darwinian concept of evolution suggests that all modern life shares a single common ancestor, often referred to as the last universal common ancestor (LUCA). Throughout evolutionary history, this ancestor has for the most part generated descendants as successive bifurcations in a tree-like manner. This so called Tree of Life, and phylogenetics in general provides much of the framework for the field of molecular evolution. Taxonomic trees allow us to better understand relationships and commonalities shared by life. For instance, a tree may tell us whether a trait or phenotype shared between two organisms is the result of shared-common ancestry (termed homologous traits) or whether the trait has evolved multiple times independent of ancestry (analogous traits such as wings).Taxonomic trees can be built using diverse sources of information. These can include morphological and phenotypic data at the macro-level down to DNA and protein sequence data at the micro-level. Ideally, trees built from multiple sources of input have identical taxonomic relationships and branching patterns, and such trees are said to be congruent. In practice, however, trees built from morphological data (say, presence or absence of wings) are often different than a tree built from molecular data (DNA or protein sequences). This requires the biologist to determine which of the two data sets is misleading and/or which taxonomic tree-building algorithm is most appropriate to use for a particular data set. Such an artform is common in the field of molecular evolution because rarely are trees congruent when built from two sources of input data.In light of this fact, we have provided the quote at the beginning of this article as a reflection about the field of molecular evolution and its interpretations of taxonomic trees. Although Reagan was not speaking about taxonomic trees in his quote, the same sort of disconnect exists between evolutionary biologists and molecular biologists (Woese and Goldenfeld 2009), as it did between conservationists and Ronald Reagan. A molecular biologist may be inclined to say that once you have seen one phylogenetic tree, you have seen them all. And in fairness, there is some validity to such a notion because historically a phylogenetic tree could not help a molecular biologist to better describe their system. An evolutionary biologist, however, will argue that individual trees have nuances that can dramatically alter our interpretation of evolutionary processes.We intend to show in this article that not all (taxonomic) trees look similar and describe identical evolutionary scenarios. We will discuss how our concept of the Tree of Life has changed over the past couple of decades, how trees can be interpreted, and what a tree can tell us about early life. In particular, the article will focus on the temperature conditions of early life because this topic has received much attention over the past few years as a direct result of improved DNA sequencing technology and a better understanding of molecular evolutionary processes. We will also describe how trees can be used to guide laboratory experiments in our attempt to understand ancient life. Lastly, we will discuss how phylogenetic trees will serve as the foundation for an “evolutionary synthetic biology” that should allow us to better understand the evolution of cellular pathways, macromolecular machines such as the ribosome, and other emergent properties of early life.     

Improving water use in crop production

Globally, agriculture accounts for 80-90% of all freshwater used by humans, and most of that is in crop production. In many areas, this water use is unsustainable; water supplies are also under pressure from other users and are being affected by climate change. Much effort is being made to reduce water use by crops and produce 'more crop per drop'. This paper examines water use by crops, taking particularly a physiological viewpoint, examining the underlying relationships between carbon uptake, growth and water loss. Key examples of recent progress in both assessing and improving crop water productivity are described. It is clear that improvements in both agronomic and physiological understanding have led to recent increases in water productivity in some crops. We believe that there is substantial potential for further improvements owing to the progress in understanding the physiological responses of plants to water supply, and there is considerable promise within the latest molecular genetic approaches, if linked to the appropriate environmental physiology. We conclude that the interactions between plant and environment require a team approach looking across the disciplines from genes to plants to crops in their particular environments to deliver improved water productivity and contribute to sustainability.     

Coping with multiple enemies: an integration of molecular and ecological perspectives

How plants respond to attack by the range of herbivores and pathogens that confront them in the field is the subject of considerable research by both molecular biologists and ecologists. However, in spite of the shared focus of these two bodies of research, there has been little integration between them. We consider the scope for such integration, and how greater dialogue between molecular biologists and ecologists could advance understanding of plant responses to multiple enemies.     

Tracheal bioengineering: the next steps. Proceeds of an International Society of Cell Therapy Pulmonary Cellular Therapy Signature Series Workshop,Paris, France,April 22, 2014

There has been significant and exciting recent progress in the development of bioengineering approaches for generating tracheal tissue that can be used for congenital and acquired tracheal diseases. This includes a growing clinical experience in both pediatric and adult patients with life-threatening tracheal diseases. However, not all of these attempts have been successful, and there is ongoing discussion and debate about the optimal approaches to be used. These include considerations of optimal materials, particularly use of synthetic versus biologic scaffolds, appropriate cellularization of the scaffolds, optimal surgical approaches and optimal measure of both clinical and biologic outcomes. To address these issues, the International Society of Cell Therapy convened a first-ever meeting of the leading clinicians and tracheal biologists, along with experts in regulatory and ethical affairs, to discuss and debate the issues. A series of recommendations are presented for how to best move the field ahead.     

Breeding for high water-use efficiency

There is a pressing need to improve the water-use efficiency of rain-fed and irrigated crop production. Breeding crop varieties with higher water-use efficiency is seen as providing part of the solution. Three key processes can be exploited in breeding for high water-use efficiency: (i) moving more of the available water through the crop rather than it being wasted as evaporation from the soil surface or drainage beyond the root zone or being left behind in the root zone at harvest; (ii) acquiring more carbon (biomass) in exchange for the water transpired by the crop, i.e. improving crop transpiration efficiency; (iii) partitioning more of the achieved biomass into the harvested product. The relative importance of any one of these processes will vary depending on how water availability varies during the crop cycle. However, these three processes are not independent. Targeting specific traits to improve one process may have detrimental effects on the other two, but there may also be positive interactions. Progress in breeding for improved water-use efficiency of rain-fed wheat is reviewed to illustrate the nature of some of these interactions and to highlight opportunities that may be exploited in other crops as well as potential pitfalls. For C3 species, measuring carbon isotope discrimination provides a powerful means of improving water-use efficiency of leaf gas exchange, but experience has shown that improvements in leaf-level water-use efficiency may not always translate into higher crop water-use efficiency or yield. In fact, the reverse has frequently been observed. Reasons for this are explored in some detail. Crop simulation modelling can be used to assess the likely impact on water-use efficiency and yield of changing the expression of traits of interest. Results of such simulations indicate that greater progress may be achieved by pyramiding traits so that potential negative effects of individual traits are neutralized. DNA-based selection techniques may assist in such a strategy.     

Research on potassium in agriculture: needs and prospects

This review highlights future needs for research on potassium (K) in agriculture. Current basic knowledge of K in soils and plant physiology and nutrition is discussed which is followed by sections dealing specifically with future needs for basic and applied research on K in soils, plants, crop nutrition and human and animal nutrition. The section on soils is devoted mainly to the concept of K availability. The current almost universal use of exchangeable K measurements obtained by chemical extraction of dried soil for making fertilizer recommendations is questioned in view of other dominant controlling factors which influence K acquisition from soils by plants. The need to take account of the living root which determines spatial K availability is emphasized. Modelling of K acquisition by field crops is discussed. The part played by K in most plant physiological processes is now well understood including the important role of K in retranslocation of photoassimilates needed for good crop quality. However, basic research is still needed to establish the role of K from molecular level to field management in plant stress situations in which K either acts alone or in combination with specific micronutrients. The emerging role of K in a number of biotic and abiotic stress situations is discussed including those of diseases and pests, frost, heat/drought, and salinity. Breeding crops which are highly efficient in uptake and internal use of K can be counterproductive because of the high demand for K needed to mitigate stress situations in farmers’ fields. The same is true for the need of high K contents in human and animal diets where a high K/Na ratio is desirable. The application of these research findings to practical agriculture is of great importance. The very rapid progress which is being made in elucidating the role of K particularly in relation to stress signalling by use of modern molecular biological approaches is indicative of the need for more interaction between molecular biologists and agronomists for the benefit of agricultural practice. The huge existing body of scientific knowledge of practical value of K in soils and plants presents a major challenge to improving the dissemination of this information on a global scale for use of farmers. To meet this challenge closer cooperation between scientists, the agrochemical industry, extension services and farmers is essential.