Divergent evolutionary pattern of starch biosynthetic pathway genes in grasses and dicots

Starch is the most widespread and abundant storage carbohydrate in crops and its production is critical to both crop yield and quality. As regards the starch content in the seeds of crop plants, there are distinct difference between grasses (Poaceae) and dicots. However, few studies have described the evolutionary pattern of genes in the starch biosynthetic pathway in these two groups of plants. In this study, therefore, an attempt was made to compare the evolutionary rate, gene duplication and selective pattern of the key genes involved in this pathway between the two groups, using five grasses and five dicots as materials. The results showed (i) distinct differences in patterns of gene duplication and loss between grasses and dicots; duplication in grasses mainly occurred prior to the divergence of grasses, whereas duplication mostly occurred in individual species within the dicots; there is less gene loss in grasses than in dicots; (ii) a considerably higher evolutionary rate in grasses than in dicots in most gene families analyzed; (iii) evidence of a different selective pattern between grasses and dicots; positive selection may have occurred asymmetrically in grasses in some gene families, e.g. AGPase small subunit. Therefore, we deduced that gene duplication contributes to, and a higher evolutionary rate is associated with, the higher starch content in grasses. In addition, two novel aspects of the evolution of the starch biosynthetic pathway were observed.

Evolutionary developmental biology: impact on systematic theory and practice, and the contribution of systematics

Evolutionary developmental genetics brings together systematists, morphologists and developmental geneticists; it will therefore impact on each of these component disciplines. The goals and methods of phylogenetic analysis are reviewed here, and the contribution of evolutionary developmental genetics to morphological systematics, in terms of character conceptualisation and primary homology assessment, is discussed. Evolutionary developmental genetics, like its component disciplines phylogenetic systematics and comparative morphology, is concerned with homology concepts. Phylogenetic concepts of homology and their limitations are considered here, and the need for independent homology statements at different levels of biological organisation is evaluated. The role of systematics in evolutionary developmental genetics is outlined. Phylogenetic systematics and comparative morphology will suggest effective sampling strategies to developmental geneticists. Phylogenetic systematics provides hypotheses of character evolution (including parallel evolution and convergence), stimulating investigations into the evolutionary gains and losses of morphologies. Comparative morphology identifies those structures that are not easily amenable to typological categorisation, and that may be of particular interest in terms of developmental genetics. The concepts of latent homology and genetic recall may also prove useful in the evolutionary interpretation of developmental genetic data.

The music instinct: the evolutionary basis of musicality

Why does music pervade our lives and those of all known human beings living today and in the recent past? Why do we feel compelled to engage in musical activity, or at least simply enjoy listening to music even if we choose not to actively participate? I argue that this is because musicality—communication using variations in pitch, rhythm, dynamics and timbre, by a combination of the voice, body (as in dance), and material culture—was essential to the lives of our pre-linguistic hominin ancestors. As a consequence we have inherited a desire to engage with music, even if this has no adaptive benefit for us today as a species whose communication system is dominated by spoken language. In this article I provide a summary of the arguments to support this view.

Sustainable urban development to 2050: complex transitions in the built environment of cities

The majority of the world’s population now live in cities. This poses great challenges, but also great opportunities in terms of tackling climate change, resource depletion and environmental degradation. Policy agendas have increasingly focused on how to develop and maintain ‘integrated sustainable urban development’, and a number of theoretical conceptualisations of urban transition have been formulated to help our thinking and understanding in both developed and developing countries. Drawing on examples around the world the paper aims to examine the key ‘critical success factors’ that need to be in place for cities to traverse a pathway to a more sustainable future in urban development terms by 2050. The paper explores how important the issues of ‘scale’ is in the context of complexity and fragmentation in the city’s built environment, identifies the lessons that can be learned for future sustainable urban development, and the further research which is needed to address future urban transitions to 2050.

Evolutionary dynamics of Staphylococcus aureus during progression from carriage to disease

Whole-genome sequencing offers new insights into the evolution of bacterial pathogens and the etiology of bacterial disease. Staph- ylococcus aureus is a major cause of bacteria-associated mortality and invasive disease and is carried asymptomatically by 27% of adults. Eighty percent of bacteremias match the carried strain. How- ever, the role of evolutionary change in the pathogen during the progression from carriage to disease is incompletely understood. Here we use high-throughput genome sequencing to discover the genetic changes that accompany the transition from nasal carriage to fatal bloodstream infection in an individual colonized with meth- icillin-sensitive S. aureus. We found a single, cohesive population exhibiting a repertoire of 30 single-nucleotide polymorphisms and four insertion/deletion variants. Mutations accumulated at a steady rate over a 13-mo period, except for a cluster of mutations preceding the transition to disease. Although bloodstream bacteria differed by just eight mutations from the original nasally carried bacteria, half of those mutations caused truncation of proteins, including a prema- ture stop codon in an AraC-family transcriptional regulator that has been implicated in pathogenicity. Comparison with evolution in two asymptomatic carriers supported the conclusion that clusters of pro- tein-truncating mutations are highly unusual. Our results demon- strate that bacterial diversity in vivo is limited but nonetheless detectable by whole-genome sequencing, enabling the study of evolutionary dynamics within the host. Regulatory or structural changes that occur during carriage may be functionally important for pathogenesis; therefore identifying those changes is a crucial step in understanding the biological causes of invasive bacterial disease.

Forecasting extinction risk of ectotherms under climate warming: an evolutionary perspective

1. It has been postulated that climate warming may pose the greatest threat species in the tropics, where ectotherms have evolved more thermal specialist physiologies. Although species could rapidly respond to environmental change through adaptation, little is known about the potential for thermal adaptation, especially in tropical species. 2. In the light of the limited empirical evidence available and predictions from mutation-selection theory, we might expect tropical ectotherms to have limited genetic variance to enable adaptation. However, as a consequence of thermodynamic constraints, we might expect this disadvantage to be at least partially offset by a fitness advantage, that is, the ‘hotter-is-better’ hypothesis. 3. Using an established quantitative genetics model and metabolic scaling relationships, we integrate the consequences of the opposing forces of thermal specialization and thermodynamic constraints on adaptive potential by evaluating extinction risk under climate warming. We conclude that the potential advantage of a higher maximal development rate can in theory more than offset the potential disadvantage of lower genetic variance associated with a thermal specialist strategy. 4. Quantitative estimates of extinction risk are fundamentally very sensitive to estimates of generation time and genetic variance. However, our qualitative conclusion that the relative risk of extinction is likely to be lower for tropical species than for temperate species is robust to assumptions regarding the effects of effective population size, mutation rate and birth rate per capita. 5. With a view to improving ecological forecasts, we use this modelling framework to review the sensitivity of our predictions to the model’s underpinning theoretical assumptions and the empirical basis of macroecological patterns that suggest thermal specialization and fitness increase towards the tropics. We conclude by suggesting priority areas for further empirical research.

The coupled δ13C-radiocarbon systematics of three Late Glacial/early Holocene speleothems: insights into soil and caveprocesses at climatic transitions

The coupled δ13C-radiocarbon systematics of threeEuropean stalagmites deposited during the Late Glacial and early Holocene were investigated to understand better how the carbon isotope systematics of speleothems respond to climate transitions. The emphasis is on understanding how speleothems may record climate-driven changes in the proportions of biogenic (soil carbon) and limestone bedrock derived carbon. At two of the three sites, the combined δ13C and 14C data argue against greater inputs of limestone carbon as the sole cause of the observed shift to higher δ13C during the cold Younger Dryas. In these stalagmites (GAR-01 from La Garma cave, N. Spain and So-1 from Sofular cave, Turkey), the combined changes in δ13C and initial 14C activities suggest enhanced decomposition of old stored, more recalcitrant, soil carbon at the onset of the warmer early Holocene. Alternative explanations involving gradual temporal changes between open- and closed-system behaviour during the Late Glacial are difficult to reconcile with observed changes in speleothem δ13C and the growth rates. In contrast, a stalagmite from Pindal cave (N. Spain) indicates an abrupt change in carbon inputs linked to local hydrological and disequilibrium isotope fractionation effects, rather than climate change. For the first time, it is shown that while the initial 14C activities of all three stalagmites broadly follow the contemporaneous atmospheric 14C trends (the Younger Dryas atmospheric 14C anomaly can be clearly discerned), subtle changes in speleothem initial 14C activities are linked to climate-driven changes in soil carbon turnover at a climate transition.

Young people’s caring relations and transitions within families affected by HIV

This chapter provides insight into young people’s caring relations and transitions within what is often considered a particularly ‘troubling’ familial context in both the global North and South: living with HIV. I analyse the findings from two qualitative studies of young people’s caring roles in families affected by HIV in the UK, Tanzania and Uganda from the perspective of a feminist ethics of care, emotion work and life course transitions.

Spin-canted antiferromagnetic phase transitions in alternating phenoxo- and carboxylato-bridged Mn(III)-salen complexes

Three new MnIII complexes, {[Mn-2(salen)(2)(OCn)](ClO4)}(n) (1), {[Mn-2(salen)(2)(OPh)](ClO4)}(n) (2) and {[Mn-2(salen)(2)(OBz)](ClO4)}(2) (3) (where salen = N,N'-bis(salicylidene)-1,2-diaminoethane dianion, OCn = cinnamate, OPh = phenylacetate and OBz = benzoate), have been synthesized and characterized structurally and magnetically. The crystal structures reveal that all three structures contain syn-anti carboxylatebridged dimeric [Mn-2(salen)(2)(OOCR)](+) cations (OOCR = bridging carboxylate) that are joined together by weak Mn center dot center dot center dot O(phenoxo) interactions to form infinite alternating chain structures in 1 and 2, but the relatively long Mn center dot center dot center dot O(phenoxo) distance [3.621(2)angstrom] in 3 restricts this structure to tetranuclear units. Magnetic studies showed that 1 and 2 exhibited magnetic long-range order at T-N = 4.0 and 4.6 K (T-N = Neel transition temperature), respectively, to give spin-canted antiferromagnetic structures. Antiferromagnetic coupling was also observed in 3 but no peaks were recorded in the field-cooled magnetization (FCM) or zero-field-cooled magnetization (ZFCM) data, indicating that 3 remained paramagnetic down to 2 K. This dominant antiferromagnetic coupling is attributed to the carboxylate bridges. The ferromagnetic coupling expected due to the Mn-O(phenoxo)center dot center dot center dot Mn bridge plays an auxiliary role in the magnetic chain, but is an essential component of the bulk magnetic properties of the material.

Transitions towards co-management: the process of marine resource management devolution in three east African countries

Communities are increasingly empowered with the ability and responsibility of working with national governments to make decisions about marine resources in decentralized co-management arrangements. This transition toward decentralized management represents a changing governance landscape. This paper explores the transition to decentralisation in marine resource management systems in three East African countries. The paper draws upon expert opinion and literature from both political science and linked social-ecological systems fields to guide exploration of five key governance transition concepts in each country: (1) drivers of change; (2) institutional arrangments; (3 institutional fit; (4) actor interactions; and (5) adaptive management. Key findings are that decentralized management in the region was largely donor-driven and only partly tranferred power to local stakeholders. However, increased accountability created a degree of democracy in regards to natural resource governance that was not previously present. Additionally, increased local-level adaptive management has emerged in most systems and, to date, this experimental management has helped to change resource user's views from metaphysical to more scientific cause-and-effect attribution of changes to resource conditions.

SANS/WANS time-resolving neutron scattering studies of polymer phase transitions using NIMROD

We use new neutron scattering instrumentation to follow in a single quantitative time-resolving experiment, the three key scales of structural development which accompany the crystallisation of synthetic polymers. These length scales span 3 orders of magnitude of the scattering vector. The study of polymer crystallisation dates back to the pioneering experiments of Keller and others who discovered the chain-folded nature of the thin lamellae crystals which are normally found in synthetic polymers. The inherent connectivity of polymers makes their crystallisation a multiscale transformation. Much understanding has developed over the intervening fifty years but the process has remained something of a mystery. There are three key length scales. The chain folded lamellar thickness is ~ 10nm, the crystal unit cell is ~ 1nm and the detail of the chain conformation is ~ 0.1nm. In previous work these length scales have been addressed using different instrumention or were coupled using compromised geometries. More recently researchers have attempted to exploit coupled time-resolved small-angle and wide-angle x-ray experiments. These turned out to be challenging experiments much related to the challenge of placing the scattering intensity on an absolute scale. However, they did stimulate the possibility of new phenomena in the very early stages of crystallisation. Although there is now considerable doubt on such experiments, they drew attention to the basic question as to the process of crystallisation in long chain molecules. We have used NIMROD on the second target station at ISIS to follow all three length scales in a time-resolving manner for poly(e-caprolactone). The technique can provide a single set of data from 0.01 to 100Å-1 on the same vertical scale. We present the results using a multiple scale model of the crystallisation process in polymers to analyse the results.

Femtosecond pulse shaping using differential evolutionary algorithm and wavelet operators

Evolutionary meta-algorithms for pulse shaping of broadband femtosecond duration laser pulses are proposed. The genetic algorithm searching the evolutionary landscape for desired pulse shapes consists of a population of waveforms (genes), each made from two concatenated vectors, specifying phases and magnitudes, respectively, over a range of frequencies. Frequency domain operators such as mutation, two-point crossover average crossover, polynomial phase mutation, creep and three-point smoothing as well as a time-domain crossover are combined to produce fitter offsprings at each iteration step. The algorithm applies roulette wheel selection; elitists and linear fitness scaling to the gene population. A differential evolution (DE) operator that provides a source of directed mutation and new wavelet operators are proposed. Using properly tuned parameters for DE, the meta-algorithm is used to solve a waveform matching problem. Tuning allows either a greedy directed search near the best known solution or a robust search across the entire parameter space.

Response of the northern stratospheric polar vortex to the seasonal alignment of QBO phase transitions

This study considers the strength of the Northern Hemisphere Holton-Tan effect (HTE) in terms of the phase alignment of the quasi-biennial oscillation (QBO) with respect to the annual cycle. Using the ERA-40 Reanalysis, it is found that the early winter (Nov–Dec) and late winter (Feb–Mar) relation between QBO phase and the strength of the stratospheric polar vortex is optimized for subsets of the 44-year record that are chosen on the basis of the seasonality of QBO phase transitions at the 30 hPa level. The timing of phase transitions serves as a proxy for changes in the vertical structure of the QBO over the whole depth of the tropical stratosphere. The statistical significance of the Nov–Dec (Feb–Mar) HTE is greatest when 30 hPa QBO phase transitions occur 9–14 (4–9) months prior to the January of the NH winter in question. This suggests that there exists for both early and late winter a vertical structure of tropical stratospheric winds that is most effective at influencing the interannual variability of the polar vortex, and that an early (late) winter HTE is associated with an early (late) progression of QBO phase towards that structure. It is also shown that the seasonality of QBO phase transitions at 30 hPa varies on a decadal timescale, with transitions during the first half of the calendar year being relatively more common during the first half of the tropical radiosonde wind record. Combining these two results suggests that decadal changes in HTE strength could result from the changing seasonality of QBO phase transitions. Citation: Anstey, J. A., and T. G. Shepherd (2008), Response of the northern stratospheric polar vortex to the seasonal alignment of QBO phase transitions, Geophys. Res. Lett., 35, L22810, doi:10.1029/2008GL035721.

City futures: exploring urban retrofit and sustainable transitions

Cities are responsible for up to 70% of global carbon emissions and 75% of global energy consumption. By 2050 it is estimated that 70% of the world's population will live in cities. The critical challenge for contemporary urbanism, therefore, is to understand how to develop the knowledge, capacity and capability for public agencies, the private sector and multiple users in city-regions (i.e. the city and its wider hinterland) to re-engineer systemically their built environment and urban infrastructure in response to climate change and resource constraints. To inform transitions to urban sustainability, key stakeholders' perceptions were sought though a participatory backcasting and scenario foresight process in order to illuminate challenging but realistic socio-technical scenarios for the systemic retrofit of core UK city-regions. The challenge of conceptualizing complex urban transitions is explored across multiple socio-technical ‘regimes’ (housing, non-domestic buildings, urban infrastructure), scales (building, neighbourhood, city-region), and domains (energy, water, use of resources) within a participatory process. The development of three archetypal ‘guiding visions’ of retrofit city-regional futures developed through this process are discussed, along with the contribution that such foresight processes might play in ‘opening up’ the governance and strategic navigation of urban sustainability.