Showing papers in "Philosophical Transactions of the Royal Society B in 2013"
TL;DR: Improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N2O (and N2) emission in order to obtain robust field and laboratory datasets for different ecosystem types.
Abstract: Although it is well established that soils are the dominating source for atmospheric nitrous oxide (N2O), we are still struggling to fully understand the complexity of the underlying microbial production and consumption processes and the links to biotic (e.g. inter- and intraspecies competition, food webs, plant–microbe interaction) and abiotic (e.g. soil climate, physics and chemistry) factors. Recent work shows that a better understanding of the composition and diversity of the microbial community across a variety of soils in different climates and under different land use, as well as plant–microbe interactions in the rhizosphere, may provide a key to better understand the variability of N2O fluxes at the soil–atmosphere interface. Moreover, recent insights into the regulation of the reduction of N2O to dinitrogen (N2) have increased our understanding of N2O exchange. This improved process understanding, building on the increased use of isotope tracing techniques and metagenomics, needs to go along with improvements in measurement techniques for N2O (and N2) emission in order to obtain robust field and laboratory datasets for different ecosystem types. Advances in both fields are currently used to improve process descriptions in biogeochemical models, which may eventually be used not only to test our current process understanding from the microsite to the field level, but also used as tools for up-scaling emissions to landscapes and regions and to explore feedbacks of soil N2O emissions to changes in environmental conditions, land management and land use.
1,871 citations
TL;DR: In the ocean, the lifetime of Nr is less well known but seems to be longer than in terrestrial ecosystems and may represent an important long-term source of N2O that will respond very slowly to control measures on the sources of NR from which it is produced.
Abstract: Global nitrogen fixation contributes 413 Tg of reactive nitrogen (Nr) to terrestrial and marine ecosystems annually of which anthropogenic activities are responsible for half, 210 Tg N. The majority of the transformations of anthropogenic Nr are on land (240 Tg N yr−1) within soils and vegetation where reduced Nr contributes most of the input through the use of fertilizer nitrogen in agriculture. Leakages from the use of fertilizer Nr contribute to nitrate (NO3−) in drainage waters from agricultural land and emissions of trace Nr compounds to the atmosphere. Emissions, mainly of ammonia (NH3) from land together with combustion related emissions of nitrogen oxides (NOx), contribute 100 Tg N yr−1 to the atmosphere, which are transported between countries and processed within the atmosphere, generating secondary pollutants, including ozone and other photochemical oxidants and aerosols, especially ammonium nitrate (NH4NO3) and ammonium sulfate (NH4)2SO4. Leaching and riverine transport of NO3 contribute 40–70 Tg N yr−1 to coastal waters and the open ocean, which together with the 30 Tg input to oceans from atmospheric deposition combine with marine biological nitrogen fixation (140 Tg N yr−1) to double the ocean processing of Nr. Some of the marine Nr is buried in sediments, the remainder being denitrified back to the atmosphere as N2 or N2O. The marine processing is of a similar magnitude to that in terrestrial soils and vegetation, but has a larger fraction of natural origin. The lifetime of Nr in the atmosphere, with the exception of N2O, is only a few weeks, while in terrestrial ecosystems, with the exception of peatlands (where it can be 102–103 years), the lifetime is a few decades. In the ocean, the lifetime of Nr is less well known but seems to be longer than in terrestrial ecosystems and may represent an important long-term source of N2O that will respond very slowly to control measures on the sources of Nr from which it is produced.
1,330 citations
TL;DR: An overview of the impact of nitrogen on the environment and human health is provided, including an assessment of the magnitude of different environmental problems, and the relative importance of Nr as a contributor to each problem.
Abstract: The demand for more food is increasing fertilizer and land use, and the demand for more energy is increasing fossil fuel combustion, leading to enhanced losses of reactive nitrogen (Nr) to the environment. Many thresholds for human and ecosystem health have been exceeded owing to Nr pollution, including those for drinking water (nitrates), air quality (smog, particulate matter, ground-level ozone), freshwater eutrophication, biodiversity loss, stratospheric ozone depletion, climate change and coastal ecosystems (dead zones). Each of these environmental effects can be magnified by the ‘nitrogen cascade’: a single atom of Nr can trigger a cascade of negative environmental impacts in sequence. Here, we provide an overview of the impact of Nr on the environment and human health, including an assessment of the magnitude of different environmental problems, and the relative importance of Nr as a contributor to each problem. In some cases, Nr loss to the environment is the key driver of effects (e.g. terrestrial and coastal eutrophication, nitrous oxide emissions), whereas in some other situations nitrogen represents a key contributor exacerbating a wider problem (e.g. freshwater pollution, biodiversity loss). In this way, the central role of nitrogen can remain hidden, even though it actually underpins many trans-boundary pollution problems.
632 citations
TL;DR: This work estimates terrestrial BNF for a pre-industrial world by combining information on N fluxes with 15N relative abundance data for terrestrial ecosystems, and suggests that the magnitude of human alternation of the N cycle is substantially larger than has been assumed.
Abstract: New techniques have identified a wide range of organisms with the capacity to carry out biological nitrogen fixation (BNF)—greatly expanding our appreciation of the diversity and ubiquity of N fixers—but our understanding of the rates and controls of BNF at ecosystem and global scales has not advanced at the same pace. Nevertheless, determining rates and controls of BNF is crucial to placing anthropogenic changes to the N cycle in context, and to understanding, predicting and managing many aspects of global environmental change. Here, we estimate terrestrial BNF for a pre-industrial world by combining information on N fluxes with 15N relative abundance data for terrestrial ecosystems. Our estimate is that pre-industrial N fixation was 58 (range of 40–100) Tg N fixed yr−1; adding conservative assumptions for geological N reduces our best estimate to 44 Tg N yr−1. This approach yields substantially lower estimates than most recent calculations; it suggests that the magnitude of human alternation of the N cycle is substantially larger than has been assumed.
566 citations
TL;DR: Advances in understanding of natural epigenetic reprogramming are beginning to aid enhancement of experimental reprograming in which the role of potential mechanisms can be investigated in vitro, and insights into in vitro repprogramming techniques may aid the understanding of epigeneticReprogramming in the germline.
Abstract: In mammalian development, epigenetic modifications, including DNA methylation patterns, play a crucial role in defining cell fate but also represent epigenetic barriers that restrict developmental potential. At two points in the life cycle, DNA methylation marks are reprogrammed on a global scale, concomitant with restoration of developmental potency. DNA methylation patterns are subsequently re-established with the commitment towards a distinct cell fate. This reprogramming of DNA methylation takes place firstly on fertilization in the zygote, and secondly in primordial germ cells (PGCs), which are the direct progenitors of sperm or oocyte. In each reprogramming window, a unique set of mechanisms regulates DNA methylation erasure and re-establishment. Recent advances have uncovered roles for the TET3 hydroxylase and passive demethylation, together with base excision repair (BER) and the elongator complex, in methylation erasure from the zygote. Deamination by AID, BER and passive demethylation have been implicated in reprogramming in PGCs, but the process in its entirety is still poorly understood. In this review, we discuss the dynamics of DNA methylation reprogramming in PGCs and the zygote, the mechanisms involved and the biological significance of these events. Advances in our understanding of such natural epigenetic reprogramming are beginning to aid enhancement of experimental reprogramming in which the role of potential mechanisms can be investigated in vitro. Conversely, insights into in vitro reprogramming techniques may aid our understanding of epigenetic reprogramming in the germline and supply important clues in reprogramming for therapies in regenerative medicine.
414 citations
TL;DR: There are 18 mammalian cytochrome P450 (CYP) families, which encode 57 genes in the human genome, but the CYP2, CYP3 and CYP4 families contain far more genes than the other 15 families; these three families are also the ones that are dramatically larger in rodent genomes.
Abstract: There are 18 mammalian cytochrome P450 (CYP) families, which encode 57 genes in the human genome. CYP2, CYP3 and CYP4 families contain far more genes than the other 15 families; these three families are also the ones that are dramatically larger in rodent genomes. Most (if not all) genes in the CYP1, CYP2, CYP3 and CYP4 families encode enzymes involved in eicosanoid metabolism and are inducible by various environmental stimuli (i.e. diet, chemical inducers, drugs, pheromones, etc.), whereas the other 14 gene families often have only a single member, and are rarely if ever inducible or redundant. Although the CYP2 and CYP3 families can be regarded as largely redundant and promiscuous, mutations or other defects in one or more genes of the remaining 16 gene families are primarily the ones responsible for P450-specific diseases-confirming these genes are not superfluous or promiscuous but rather are more directly involved in critical life functions. P450-mediated diseases comprise those caused by: aberrant steroidogenesis; defects in fatty acid, cholesterol and bile acid pathways; vitamin D dysregulation and retinoid (as well as putative eicosanoid) dysregulation during fertilization, implantation, embryogenesis, foetogenesis and neonatal development.
404 citations
TL;DR: Some of the key directions of eQTL research are discussed, namely, the discovery of genetic variants that explain variation in gene expression levels, and their implications.
Abstract: The last few years have seen the development of large efforts for the analysis of genome function, especially in the context of genome variation. One of the most prominent directions has been the extensive set of studies on expression quantitative trait loci (eQTLs), namely, the discovery of genetic variants that explain variation in gene expression levels. Such studies have offered promise not just for the characterization of functional sequence variation but also for the understanding of basic processes of gene regulation and interpretation of genome-wide association studies. In this review, we discuss some of the key directions of eQTL research and its implications.
385 citations
TL;DR: It is found that phylogenetic signal varies extensively across and even within trait categories, and the highest values are exhibited by brain size and body mass, while moderate values are found in the degree of territoriality and canine size dimorphism.
Abstract: Examining biological diversity in an explicitly evolutionary context has been the subject of research for several decades, yet relatively recent advances in analytical techniques and the increasing availability of species-level phylogenies, have enabled scientists to ask new questions. One such approach is to quantify phylogenetic signal to determine how trait variation is correlated with the phylogenetic relatedness of species. When phylogenetic signal is high, closely related species exhibit similar traits, and this biological similarity decreases as the evolutionary distance between species increases. Here, we first review the concept of phylogenetic signal and suggest how to measure and interpret phylogenetic signal in species traits. Second, we quantified phylogenetic signal in primates for 31 variables, including body mass, brain size, life-history, sexual selection, social organization, diet, activity budget, ranging patterns and climatic variables. We found that phylogenetic signal varies extensively across and even within trait categories. The highest values are exhibited by brain size and body mass, moderate values are found in the degree of territoriality and canine size dimorphism, while low values are displayed by most of the remaining variables. Our results have important implications for the evolution of behaviour and ecology in primates and other vertebrates.
385 citations
TL;DR: This special issue focuses on evolutionary rescue (ER), the idea that evolution might occur sufficiently fast to arrest population decline and allow population recovery before extinction ensues.
Abstract: There is concern that the rate of environmental change is now exceeding the capacity of many populations to adapt. Mitigation of biodiversity loss requires science that integrates both ecological and evolutionary responses of populations and communities to rapid environmental change, and can identify the conditions that allow the recovery of declining populations. This special issue focuses on evolutionary rescue (ER), the idea that evolution might occur sufficiently fast to arrest population decline and allow population recovery before extinction ensues. ER emphasizes a shift to a perspective on evolutionary dynamics that focuses on short time-scales, genetic variants of large effects and absolute rather than relative fitness. The contributions in this issue reflect the state of field; the articles address the latest conceptual developments, and report novel theoretical and experimental results. The examples in this issue demonstrate that this burgeoning area of research can inform problems of direct practical concern, such as the conservation of biodiversity, adaptation to climate change and the emergence of infectious disease. The continued development of research on ER will be necessary if we are to understand the extent to which anthropogenic global change will reduce the Earth's biodiversity.
347 citations
TL;DR: It is shown how measurements reveal a strong, but complex pattern of climatic dependence, which is increasingly being characterized using ground-based NH3 monitoring and satellite observations, while advances in process-based modelling are illustrated for agricultural and natural sources.
Abstract: Existing descriptions of bi-directional ammonia (NH3) land-atmosphere exchange incorporate temperature and moisture controls, and are beginning to be used in regional chemical transport models. However, such models have typically applied simpler emission factors to upscale the main NH3 emission terms. While this approach has successfully simulated the main spatial patterns on local to global scales, it fails to address the environment- and climate-dependence of emissions. To handle these issues, we outline the basis for a new modelling paradigm where both NH3 emissions and deposition are calculated online according to diurnal, seasonal and spatial differences in meteorology. We show how measurements reveal a strong, but complex pattern of climatic dependence, which is increasingly being characterized using ground-based NH3 monitoring and satellite observations, while advances in process-based modelling are illustrated for agricultural and natural sources, including a global application for seabird colonies. A future architecture for NH3 emission-deposition modelling is proposed that integrates the spatio-temporal interactions, and provides the necessary foundation to assess the consequences of climate change. Based on available measurements, a first empirical estimate suggests that 5°C warming would increase emissions by 42 per cent (28-67%). Together with increased anthropogenic activity, global NH3 emissions may increase from 65 (45-85) Tg N in 2008 to reach 132 (89-179) Tg by 2100.
330 citations
TL;DR: Recent technological advances are helping to build a functional profile of the P450 determinants of insecticide metabolic resistance in mosquitoes, which will enable the design of new insecticides with optimized efficacy in different environments.
Abstract: The fight against diseases spread by mosquitoes and other insects has enormous environmental, economic and social consequences. Chemical insecticides remain the first line of defence but the control of diseases, especially malaria and dengue fever, is being increasingly undermined by insecticide resistance. Mosquitoes have a large repertoire of P450s (over 100 genes). By pinpointing the key enzymes associated with insecticide resistance we can begin to develop new tools to aid the implementation of control interventions and reduce their environmental impact on Earth. Recent technological advances are helping us to build a functional profile of the P450 determinants of insecticide metabolic resistance in mosquitoes. Alongside, the cross-responses of mosquito P450s to insecticides and pollutants are also being investigated. Such research will provide the means to produce diagnostic tools for early detection of P450s linked to resistance. It will also enable the design of new insecticides with optimized efficacy in different environments.
TL;DR: Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell–cell fusion ofsyncytial cell layers at the fetal–maternal interface.
Abstract: The development of the emerging field of ‘paleovirology’ allows biologists to reconstruct the evolutionary history of fossil endogenous retroviral sequences integrated within the genome of living organisms and has led to the retrieval of conserved, ancient retroviral genes ‘exapted’ by ancestral hosts to fulfil essential physiological roles, syncytin genes being undoubtedly among the most remarkable examples of such a phenomenon. Indeed, syncytins are ‘new’ genes encoding proteins derived from the envelope protein of endogenous retroviral elements that have been captured and domesticated on multiple occasions and independently in diverse mammalian species, through a process of convergent evolution. Knockout of syncytin genes in mice provided evidence for their absolute requirement for placenta development and embryo survival, via formation by cell–cell fusion of syncytial cell layers at the fetal–maternal interface. These genes of exogenous origin, acquired ‘by chance’ and yet still ‘necessary’ to carry out a basic function in placental mammals, may have been pivotal in the emergence of mammalian ancestors with a placenta from egg-laying animals via the capture of a founding retroviral env gene, subsequently replaced in the diverse mammalian lineages by new env-derived syncytin genes, each providing its host with a positive selective advantage.
University College London1, University of Leeds2, University of Yaoundé I3, Center for International Forestry Research4, Smithsonian Tropical Research Institute5, University of Wisconsin–Milwaukee6, Forestry Commission7, École Normale Supérieure8, Université libre de Bruxelles9, University of Liège10, Royal Museum for Central Africa11, Ghent University12, Duke University13, London School of Economics and Political Science14, Forestry Research Institute of Ghana15, Wildlife Conservation Society16, Royal Botanic Garden Edinburgh17, American Museum of Natural History18, Austral University of Chile19, University of Stirling20, James Cook University21, University of Oxford22, University of York23, University of Agriculture, Faisalabad24, University of Cambridge25, Southern Cross University26, National University of Singapore27, University of Toronto28, University of Southampton29
TL;DR: The results indicate that AGB is mediated by both climate and soils, and suggest that the AGB of African closed-canopy tropical forests may be particularly sensitive to future precipitation and temperature changes.
Abstract: We report above-ground biomass (AGB), basal area, stem density and wood mass density estimates from 260 sample plots (mean size: 1.2 ha) in intact closed-canopy tropical forests across 12 African countries. Mean AGB is 395.7 Mg dry mass ha−1 (95% CI: 14.3), substantially higher than Amazonian values, with the Congo Basin and contiguous forest region attaining AGB values (429 Mg ha−1) similar to those of Bornean forests, and significantly greater than East or West African forests. AGB therefore appears generally higher in palaeo- compared with neotropical forests. However, mean stem density is low (426 ± 11 stems ha−1 greater than or equal to 100 mm diameter) compared with both Amazonian and Bornean forests (cf. approx. 600) and is the signature structural feature of African tropical forests. While spatial autocorrelation complicates analyses, AGB shows a positive relationship with rainfall in the driest nine months of the year, and an opposite association with the wettest three months of the year; a negative relationship with temperature; positive relationship with clay-rich soils; and negative relationships with C : N ratio (suggesting a positive soil phosphorus–AGB relationship), and soil fertility computed as the sum of base cations. The results indicate that AGB is mediated by both climate and soils, and suggest that the AGB of African closed-canopy tropical forests may be particularly sensitive to future precipitation and temperature changes.
TL;DR: It is suggested that classifications of selection based on distinction between the form of competition or the components of fitness that are involved introduce unnecessary complexities and that the most useful approach in understanding the evolution and distribution of differences and similarities between the sexes is to compare the operation of selection in males and females in different reproductive systems.
Abstract: During the latter half of the last century, evidence of reproductive competition between males and male selection by females led to the development of a stereotypical view of sex differences that characterized males as competitive and aggressive, and females as passive and choosy, which is currently being revised. Here, we compare social competition and its consequences for selection in males and females and argue that similar selection processes operate in both sexes and that contrasts between the sexes are quantitative rather than qualitative. We suggest that classifications of selection based on distinction between the form of competition or the components of fitness that are involved introduce unnecessary complexities and that the most useful approach in understanding the evolution and distribution of differences and similarities between the sexes is to compare the operation of selection in males and females in different reproductive systems.
TL;DR: There is a better understanding of the mechanistic basis of DNA demethylation during epigenetic reprogramming in primordial germ cells and during pre-implantation development.
Abstract: DNA methylation is dynamically remodelled during the mammalian life cycle through distinct phases of reprogramming and de novo methylation. These events enable the acquisition of cellular potential followed by the maintenance of lineage-restricted cell identity, respectively, a process that defines the life cycle through successive generations. DNA methylation contributes to the epigenetic regulation of many key developmental processes including genomic imprinting, X-inactivation, genome stability and gene regulation. Emerging sequencing technologies have led to recent insights into the dynamic distribution of DNA methylation during development and the role of this epigenetic mark within distinct genomic contexts, such as at promoters, exons or imprinted control regions. Additionally, there is a better understanding of the mechanistic basis of DNA demethylation during epigenetic reprogramming in primordial germ cells and during pre-implantation development. Here, we discuss our current understanding of the developmental roles and dynamics of this key epigenetic system.
TL;DR: Neither the standing genetic variation of small populations nor the mutation supply of large populations, however, may be sufficient to provide evolutionary rescue for most populations.
Abstract: Populations subject to severe stress may be rescued by natural selection, but its operation is restricted by ecological and genetic constraints. The cost of natural selection expresses the limited capacity of a population to sustain the load of mortality or sterility required for effective selection. Genostasis expresses the lack of variation that prevents many populations from adapting to stress. While the role of relative fitness in adaptation is well understood, evolutionary rescue emphasizes the need to recognize explicitly the importance of absolute fitness. Permanent adaptation requires a range of genetic variation in absolute fitness that is broad enough to provide a few extreme types capable of sustained growth under a stress that would cause extinction if they were not present. This principle implies that population size is an important determinant of rescue. The overall number of individuals exposed to selection will be greater when the population declines gradually under a constant stress, or is progressively challenged by gradually increasing stress. In gradually deteriorating environments, survival at lethal stress may be procured by prior adaptation to sublethal stress through genetic correlation. Neither the standing genetic variation of small populations nor the mutation supply of large populations, however, may be sufficient to provide evolutionary rescue for most populations.
TL;DR: An orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.
Abstract: Organohalide respiration is an anaerobic bacterial respiratory process that uses halogenated hydrocarbons as terminal electron acceptors during electron transport-based energy conservation. This dechlorination process has triggered considerable interest for detoxification of anthropogenic groundwater contaminants. Organohalide-respiring bacteria have been identified from multiple bacterial phyla, and can be categorized as obligate and non-obligate organohalide respirers. The majority of the currently known organohalide-respiring bacteria carry multiple reductive dehalogenase genes. Analysis of a curated set of reductive dehalogenases reveals that sequence similarity and substrate specificity are generally not correlated, making functional prediction from sequence information difficult. In this article, an orthologue-based classification system for the reductive dehalogenases is proposed to aid integration of new sequencing data and to unify terminology.
TL;DR: Examples of how the genetic and functional diversification of plant P450s drives chemical diversity in light of plant evolution are discussed.
Abstract: The irreversible nature of reactions catalysed by P450s makes these enzymes landmarks in the evolution of plant metabolic pathways. Founding members of P450 families are often associated with general (i.e. primary) metabolic pathways, restricted to single copy or very few representatives, indicative of purifying selection. Recruitment of those and subsequent blooms into multi-member gene families generates genetic raw material for functional diversification, which is an inherent characteristic of specialized (i.e. secondary) metabolism. However, a growing number of highly specialized P450s from not only the CYP71 clan indicate substantial contribution of convergent and divergent evolution to the observed general and specialized metabolite diversity. We will discuss examples of how the genetic and functional diversification of plant P450s drives chemical diversity in light of plant evolution. Even though it is difficult to predict the function or substrate of a P450 based on sequence similarity, grouping with a family or subfamily in phylogenetic trees can indicate association with metabolism of particular classes of compounds. Examples will be given that focus on multi-member gene families of P450s involved in the metabolic routes of four classes of specialized metabolites: cyanogenic glucosides, glucosinolates, mono- to triterpenoids and phenylpropanoids.
TL;DR: It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer ‘cognitive surplus’ through crowdsourcing.
Abstract: The primary aim of this review was to evaluate the state of knowledge of the geographical distribution of all infectious diseases of clinical significance to humans. A systematic review was conducted to enumerate cartographic progress, with respect to the data available for mapping and the methods currently applied. The results helped define the minimum information requirements for mapping infectious disease occurrence, and a quantitative framework for assessing the mapping opportunities for all infectious diseases. This revealed that of 355 infectious diseases identified, 174 (49%) have a strong rationale for mapping and of these only 7 (4%) had been comprehensively mapped. A variety of ambitions, such as the quantification of the global burden of infectious disease, international biosurveillance, assessing the likelihood of infectious disease outbreaks and exploring the propensity for infectious disease evolution and emergence, are limited by these omissions. An overview of the factors hindering progress in disease cartography is provided. It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer ‘cognitive surplus’ through crowdsourcing.
TL;DR: Successful redirection of the anthocyanin biosynthesis pathway to delphinidin was achieved by expressing F3′5′H coding regions resulting in carnations and roses with novel blue hues that have been commercialized.
Abstract: Cytochromes P450 play important roles in biosynthesis of flavonoids and their coloured class of compounds, anthocyanins, both of which are major floral pigments. The number of hydroxyl groups on the B-ring of anthocyanidins (the chromophores and precursors of anthocyanins) impact the anthocyanin colour, the more the bluer. The hydroxylation pattern is determined by two cytochromes P450, flavonoid 3′-hydroxylase (F3′H) and flavonoid 3′,5′-hydroxylase (F3′5′H) and thus they play a crucial role in the determination of flower colour. F3′H and F3′5′H mostly belong to CYP75B and CYP75A, respectively, except for the F3′5′Hs in Compositae that were derived from gene duplication of CYP75B and neofunctionalization. Roses and carnations lack blue/violet flower colours owing to the deficiency of F3′5′H and therefore lack the B-ring-trihydroxylated anthocyanins based upon delphinidin. Successful redirection of the anthocyanin biosynthesis pathway to delphinidin was achieved by expressing F3′5′H coding regions resulting in carnations and roses with novel blue hues that have been commercialized. Suppression of F3′5′H and F3′H in delphinidin-producing plants reduced the number of hydroxyl groups on the anthocyanidin B-ring resulting in the production of monohydroxylated anthocyanins based on pelargonidin with a shift in flower colour to orange/red. Pelargonidin biosynthesis is enhanced by additional expression of a dihydroflavonol 4-reductase that can use the monohydroxylated dihydrokaempferol (the pelargonidin precursor). Flavone synthase II (FNSII)-catalysing flavone biosynthesis from flavanones is also a P450 (CYP93B) and contributes to flower colour, because flavones act as co-pigments to anthocyanins and can cause blueing and darkening of colour. However, transgenic plants expression of a FNSII gene yielded paler flowers owing to a reduction of anthocyanins because flavanones are precursors of anthocyanins and flavones.
TL;DR: Human females have a particular proclivity for using indirect aggression, which is typically directed at other females, especially attractive and sexually available females, in the context of intrasexual competition for mates.
Abstract: Indirect aggression includes behaviours such as criticizing a competitor's appearance, spreading rumours about a person's sexual behaviour and social exclusion Human females have a particular proclivity for using indirect aggression, which is typically directed at other females, especially attractive and sexually available females, in the context of intrasexual competition for mates Indirect aggression is an effective intrasexual competition strategy It is associated with a diminished willingness to compete on the part of victims and with greater dating and sexual behaviour among those who perpetrate the aggression
TL;DR: It is shown that mats have enhanced productivity in experiments and more expansive covers in situ under projected near-future CO2 conditions both in temperate and tropical conditions, and awareness is raised of CO2 as a resource whose change in availability could have wide-ranging community consequences beyond its direct effects.
Abstract: Predictions concerning the consequences of the oceanic uptake of increasing atmospheric carbon dioxide (CO2) have been primarily occupied with the effects of ocean acidification on calcifying organisms, particularly those critical to the formation of habitats (e.g. coral reefs) or their maintenance (e.g. grazing echinoderms). This focus overlooks direct and indirect effects of CO2 on non-calcareous taxa that play critical roles in ecosystem shifts (e.g. competitors). We present the model that future atmospheric [CO2] may act as a resource for mat-forming algae, a diverse and widespread group known to reduce the resilience of kelp forests and coral reefs. We test this hypothesis by combining laboratory and field CO2 experiments and data from ‘natural’ volcanic CO2 vents. We show that mats have enhanced productivity in experiments and more expansive covers in situ under projected near-future CO2 conditions both in temperate and tropical conditions. The benefits of CO2 are likely to vary among species of producers, potentially leading to shifts in species dominance in a high CO2 world. We explore how ocean acidification combines with other environmental changes across a number of scales, and raise awareness of CO2 as a resource whose change in availability could have wide-ranging community consequences beyond its direct effects.
TL;DR: This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells, and focuses on the main evolutionary transitions in early bioenergetic evolution.
Abstract: Life is the harnessing of chemical energy in such a way that the energy-harnessing device makes a copy of itself. This paper outlines an energetically feasible path from a particular inorganic setting for the origin of life to the first free-living cells. The sources of energy available to early organic synthesis, early evolving systems and early cells stand in the foreground, as do the possible mechanisms of their conversion into harnessable chemical energy for synthetic reactions. With regard to the possible temporal sequence of events, we focus on: (i) alkaline hydrothermal vents as the far-from-equilibrium setting, (ii) the Wood–Ljungdahl (acetyl-CoA) pathway as the route that could have underpinned carbon assimilation for these processes, (iii) biochemical divergence, within the naturally formed inorganic compartments at a hydrothermal mound, of geochemically confined replicating entities with a complexity below that of free-living prokaryotes, and (iv) acetogenesis and methanogenesis as the ancestral forms of carbon and energy metabolism in the first free-living ancestors of the eubacteria and archaebacteria, respectively. In terms of the main evolutionary transitions in early bioenergetic evolution, we focus on: (i) thioester-dependent substrate-level phosphorylations, (ii) harnessing of naturally existing proton gradients at the vent–ocean interface via the ATP synthase, (iii) harnessing of Na+ gradients generated by H+/Na+ antiporters, (iv) flavin-based bifurcation-dependent gradient generation, and finally (v) quinone-based (and Q-cycle-dependent) proton gradient generation. Of those five transitions, the first four are posited to have taken place at the vent. Ultimately, all of these bioenergetic processes depend, even today, upon CO2 reduction with low-potential ferredoxin (Fd), generated either chemosynthetically or photosynthetically, suggesting a reaction of the type ‘reduced iron → reduced carbon’ at the beginning of bioenergetic evolution.
TL;DR: Analysis of variance over the Congo Basin is used to show that expanding agriculture and increasing fuelwood demands are key drivers of deforestation in the region, whereas well-controlled timber exploitation programmes have little or no direct influence on forest-cover reduction at present.
Abstract: This paper presents a map of Africa's rainforests for 2005. Derived from moderate resolution imaging spectroradiometer data at a spatial resolution of 250 m and with an overall accuracy of 84%, this map provides new levels of spatial and thematic detail. The map is accompanied by measurements of deforestation between 1990, 2000 and 2010 for West Africa, Central Africa and Madagascar derived from a systematic sample of Landsat images—imagery from equivalent platforms is used to fill gaps in the Landsat record. Net deforestation is estimated at 0.28% yr−1 for the period 1990–2000 and 0.14% yr−1 for the period 2000–2010. West Africa and Madagascar exhibit a much higher deforestation rate than the Congo Basin, for example, three times higher for West Africa and nine times higher for Madagascar. Analysis of variance over the Congo Basin is then used to show that expanding agriculture and increasing fuelwood demands are key drivers of deforestation in the region, whereas well-controlled timber exploitation programmes have little or no direct influence on forest-cover reduction at present. Rural and urban population concentrations and fluxes are also identified as strong underlying causes of deforestation in this study.
TL;DR: Polyandry can reduce a male's ability to monopolize females, and thus weaken male focused sexual selection, and estimates of sexual selection intensity rely heavily on measures of male mating success, but polyandry now raises serious questions over the validity of such approaches.
Abstract: The Darwin–Bateman paradigm recognizes competition among males for access to multiple mates as the main driver of sexual selection. Increasingly, however, females are also being found to benefit from multiple mating so that polyandry can generate competition among females for access to multiple males, and impose sexual selection on female traits that influence their mating success. Polyandry can reduce a male's ability to monopolize females, and thus weaken male focused sexual selection. Perhaps the most important effect of polyandry on males arises because of sperm competition and cryptic female choice. Polyandry favours increased male ejaculate expenditure that can affect sexual selection on males by reducing their potential reproductive rate. Moreover, sexual selection after mating can ameliorate or exaggerate sexual selection before mating. Currently, estimates of sexual selection intensity rely heavily on measures of male mating success, but polyandry now raises serious questions over the validity of such approaches. Future work must take into account both pre- and post-copulatory episodes of selection. A change in focus from the products of sexual selection expected in males, to less obvious traits in females, such as sensory perception, is likely to reveal a greater role of sexual selection in female evolution.
TL;DR: Recent knowledge on processes forming NO in soils and the factors controlling its emission to the atmosphere are reviewed and schemes for simulating these processes are described, and the results are discussed with the purpose of scaling up to global emission.
Abstract: Nitric oxide (NO) is a reactive gas that plays an important role in atmospheric chemistry by influencing the production and destruction of ozone and thereby the oxidizing capacity of the atmosphere. NO also contributes by its oxidation products to the formation of acid rain. The major sources of NO in the atmosphere are anthropogenic emissions (from combustion of fossil fuels) and biogenic emission from soils. NO is both produced and consumed in soils as a result of biotic and abiotic processes. The main processes involved are microbial nitrification and denitrification, and chemodenitrification. Thus, the net result is complex and dependent on several factors such as nitrogen availability, organic matter content, oxygen status, soil moisture, pH and temperature. This paper reviews recent knowledge on processes forming NO in soils and the factors controlling its emission to the atmosphere. Schemes for simulating these processes are described, and the results are discussed with the purpose of scaling up to global emission.
TL;DR: Soil nitrogen budgets are used in a global, distributed flow-path model and results indicate that riparian buffer zones are an important source of N2O contributing an estimated 0.9 Tg N2N–N yr−1 in 2000, much more important than groundwater and riparian zones in controlling the N flow to rivers and the oceans.
Abstract: Soil nitrogen (N) budgets are used in a global, distributed flow-path model with 0.5° × 0.5° resolution, representing denitrification and N2O emissions from soils, groundwater and riparian zones for the period 1900–2000 and scenarios for the period 2000–2050 based on the Millennium Ecosystem Assessment. Total agricultural and natural N inputs from N fertilizers, animal manure, biological N2 fixation and atmospheric N deposition increased from 155 to 345 Tg N yr−1 (Tg = teragram; 1 Tg = 1012 g) between 1900 and 2000. Depending on the scenario, inputs are estimated to further increase to 408–510 Tg N yr−1 by 2050. In the period 1900–2000, the soil N budget surplus (inputs minus withdrawal by plants) increased from 118 to 202 Tg yr−1, and this may remain stable or further increase to 275 Tg yr−1 by 2050, depending on the scenario. N2 production from denitrification increased from 52 to 96 Tg yr−1 between 1900 and 2000, and N2O–N emissions from 10 to 12 Tg N yr−1. The scenarios foresee a further increase to 142 Tg N2–N and 16 Tg N2O–N yr−1 by 2050. Our results indicate that riparian buffer zones are an important source of N2O contributing an estimated 0.9 Tg N2O–N yr−1 in 2000. Soils are key sites for denitrification and are much more important than groundwater and riparian zones in controlling the N flow to rivers and the oceans.
TL;DR: It is hypothesize that, in the near future, the trophic changes brought about by hunting will have a larger and more rapid impact on Central African rainforest structure and function than the direct impacts of climate change on the vegetation.
Abstract: Humans have hunted wildlife in Central Africa for millennia. Today, however, many species are being rapidly extirpated and sanctuaries for wildlife are dwindling. Almost all Central Africa's forests are now accessible to hunters. Drastic declines of large mammals have been caused in the past 20 years by the commercial trade for meat or ivory. We review a growing body of empirical data which shows that trophic webs are significantly disrupted in the region, with knock-on effects for other ecological functions, including seed dispersal and forest regeneration. Plausible scenarios for land-use change indicate that increasing extraction pressure on Central African forests is likely to usher in new worker populations and to intensify the hunting impacts and trophic cascade disruption already in progress, unless serious efforts are made for hunting regulation. The profound ecological changes initiated by hunting will not mitigate and may even exacerbate the predicted effects of climate change for the region. We hypothesize that, in the near future, the trophic changes brought about by hunting will have a larger and more rapid impact on Central African rainforest structure and function than the direct impacts of climate change on the vegetation. Immediate hunting regulation is vital for the survival of the Central African rainforest ecosystem.
TL;DR: The contribution of the early pioneers of sexual selection, Darwin and Bateman, remains generally valid, and should not be negated; as with much in science, pioneering advances are more often amplified and refined, rather than replaced with entirely new paradigms.
Abstract: We give a historic overview and critical perspective of polyandry in the context of sexual selection. Early approaches tended to obfuscate the fact that the total matings (copulations) by the two sexes is equal, neglecting female interests and that females often mate with (or receive ejaculates from) more than one male (polyandry). In recent years, we have gained much more insight into adaptive reasons for polyandry, particularly from the female perspective. However, costs and benefits of multiple mating are unlikely to be equal for males and females. These must be assessed for each partner at each potential mating between male i and female j, and will often be highly asymmetric. Interests of i and j may be in conflict, with (typically, ultimately because of primordial sex differences) i benefitting and j losing from mating, although theoretically the reverse can also obtain. Polyandry reduces the sex difference in Bateman gradients, and the probability of sexual conflict over mating by: (i) reducing the potential expected value of each mating to males in inverse proportion to the number of mates per female per clutch, and also often by (ii) increasing ejaculate costs through increased sperm allocation. It can nevertheless create conflict over fertilization and increase conflict over parental investment. The observed mean mating frequency for the population (and hence the degree of polyandry) is likely, at least in part, to reflect a resolution of sexual conflict. Immense diversity exists across and within taxa in the extent of polyandry, and views on its significance have changed radically, as we illustrate using avian polyandry as a case study. Despite recent criticisms, the contribution of the early pioneers of sexual selection, Darwin and Bateman, remains generally valid, and should not, therefore, be negated; as with much in science, pioneering advances are more often amplified and refined, rather than replaced with entirely new paradigms.
TL;DR: The need to better localize crop production and livestock breeding, on the one hand, and agriculture and food demand on the other hand, is put forward as a condition to being able to supply food to human populations while preserving environmental resources.
Abstract: The nitrogen cycle of pre-industrial ecosystems has long been remarkably closed, in spite of the high mobility of this element in the atmosphere and hydrosphere. Inter-regional and international commercial exchanges of agricultural goods, which considerably increased after the generalization of the use of synthetic nitrogen fertilizers, introduced an additional type of nitrogen mobility, which nowadays rivals the atmospheric and hydrological fluxes in intensity, and causes their enhancement at the local, regional and global scales. Eighty-five per cent of the net anthropogenic input of reactive nitrogen occurs on only 43 per cent of the land area. Modern agriculture based on the use of synthetic fertilizers and the decoupling of crop and animal production is responsible for the largest part of anthropogenic losses of reactive nitrogen to the environment. In terms of levers for better managing the nitrogen cascade, beyond technical improvement of agricultural practices tending to increase nitrogen use efficiency, or environmental engineering management measures to increase nitrogen sinks in the landscape, the need to better localize crop production and livestock breeding, on the one hand, and agriculture and food demand on the other hand, is put forward as a condition to being able to supply food to human populations while preserving environmental resources.