Evidence of neutral transcriptome evolution in plants

The transcriptome of an organism is its set of gene transcripts (mRNAs) at a defined spatial and temporal locus. Because gene expression is affected markedly by environmental and developmental perturbations, it is widely assumed that transcriptome divergence among taxa represents adaptive phenotypic selection. This assumption has been challenged by neutral theories which propose that stochastic processes drive transcriptome evolution. To test for evidence of neutral transcriptome evolution in plants, we quantified 18 494 gene transcripts in nonsenescent leaves of 14 taxa of Brassicaceae using robust cross-species transcriptomics which includes a two-step physical and in silico-based normalization procedure based on DNA similarity among taxa. Transcriptome divergence correlates positively with evolutionary distance between taxa and with variation in gene expression among samples. Results are similar for pseudogenes and chloroplast genes evolving at different rates. Remarkably, variation in transcript abundance among root-cell samples correlates positively with transcriptome divergence among root tissues and among taxa. Because neutral processes affect transcriptome evolution in plants, many differences in gene expression among or within taxa may be nonfunctional, reflecting ancestral plasticity and founder effects. Appropriate null models are required when comparing transcriptomes in space and time.

Within-host evolution of Staphylococcus aureus during asymptomatic carriage

Background Staphylococcus aureus is a major cause of healthcare associated mortality, but like many important bacterial pathogens, it is a common constituent of the normal human body flora. Around a third of healthy adults are carriers. Recent evidence suggests that evolution of S. aureus during nasal carriage may be associated with progression to invasive disease. However, a more detailed understanding of within-host evolution under natural conditions is required to appreciate the evolutionary and mechanistic reasons why commensal bacteria such as S. aureus cause disease. Therefore we examined in detail the evolutionary dynamics of normal, asymptomatic carriage. Sequencing a total of 131 genomes across 13 singly colonized hosts using the Illumina platform, we investigated diversity, selection, population dynamics and transmission during the short-term evolution of S. aureus. Principal Findings We characterized the processes by which the raw material for evolution is generated: micro-mutation (point mutation and small insertions/deletions), macro-mutation (large insertions/deletions) and the loss or acquisition of mobile elements (plasmids and bacteriophages). Through an analysis of synonymous, non-synonymous and intergenic mutations we discovered a fitness landscape dominated by purifying selection, with rare examples of adaptive change in genes encoding surface-anchored proteins and an enterotoxin. We found evidence for dramatic, hundred-fold fluctuations in the size of the within-host population over time, which we related to the cycle of colonization and clearance. Using a newly-developed population genetics approach to detect recent transmission among hosts, we revealed evidence for recent transmission between some of our subjects, including a husband and wife both carrying populations of methicillin-resistant S. aureus (MRSA). Significance This investigation begins to paint a picture of the within-host evolution of an important bacterial pathogen during its prevailing natural state, asymptomatic carriage. These results also have wider significance as a benchmark for future systematic studies of evolution during invasive S. aureus disease.

Simulations of angular momentum evolution in wind-fed CV precursors

It is thought that the secondary stars in cataclysmic variables (CVs) may undergo a period of mass loss in the form of a wind during the evolution of the system (Mullan et al. 1992). This wind is thought to magnetically brake the secondary star with a time-scale ~ 10^8 yr (e.g. van Paradijs 1986). When the secondary’s spin has been brought close to synchronism with the orbit it is possible for tidal torques to lock the secondary in synchronous rotation.

On the evolution of monopoly pricing in Internet-assisted search markets

This study examines the evolution of prices in markets with Internet price-comparison search engines. The empirical study analyzes laboratory data of prices available to informed consumers, for two industry sizes and two conditions on the sample (complete and incomplete). Distributions are typically bimodal. One of the two modes of distribution, corresponding to monopoly pricing, tends to attract such pricing strategies increasingly over time. The second one, corresponding to interior pricing, follows a decreasing trend. Monopoly pricing can serve as a means of insurance against more competitive (but riskier) behavior. In fact, experimental subjects who initially earn low profits due to interior pricing are more likely to switch to monopoly pricing than subjects who experience good returns from the start.

Antarctic Peninsula ice sheet evolution during the Cenozoic Era

The Antarctic Peninsula region is currently undergoing rapid environmental change, resulting in the thinning, acceleration and recession of glaciers and the sequential collapse of ice shelves. It is important to view these changes in the context of long-term palaeoenvironmental complexity and to understand the key processes controlling ice sheet growth and recession. In addition, numerical ice sheet models require detailed geological data for tuning and testing. Therefore, this paper systematically and holistically reviews published geological evidence for Antarctic Peninsula Ice Sheet variability for each key locality throughout the Cenozoic, and brings together the prevailing consensus of the extent, character and behaviour of the glaciations of the Antarctic Peninsula region. Major contributions include a downloadable database of 186 terrestrial and marine calibrated dates; an original reconstruction of the LGM ice sheet; and a new series of isochrones detailing ice sheet retreat following the LGM. Glaciation of Antarctica was initiated around the Eocene/Oligocene transition in East Antarctica. Palaeogene records of Antarctic Peninsula glaciation are primarily restricted to King George Island, where glacigenic sediments provide a record of early East Antarctic glaciations, but with modification of far-travelled erratics by local South Shetland Island ice caps. Evidence for Neogene glaciation is derived primarily from King George Island and James Ross Island, where glaciovolcanic strata indicate that ice thicknesses reached 500–850 m during glacials. This suggests that the Antarctic Peninsula Ice Sheet draped, rather than drowned, the topography. Marine geophysical investigations indicate multiple ice sheet advances during this time. Seismic profiling of continental shelf-slope deposits indicates up to ten large advances of the Antarctic Peninsula Ice Sheet during the Early Pleistocene, when the ice sheet was dominated by 40 kyr cycles. Glacials became more pronounced, reaching the continental shelf edge, and of longer duration during the Middle Pleistocene. During the Late Pleistocene, repeated glacials reached the shelf edge, but ice shelves inhibited iceberg rafting. The Last Glacial Maximum (LGM) occurred at 18 ka BP, after which transitional glaciomarine sediments on the continental shelf indicate ice-sheet retreat. The continental shelf contains large bathymetric troughs, which were repeatedly occupied by large ice streams during Pleistocene glaciations. Retreat after the LGM was episodic in the Weddell Sea, with multiple readvances and changes in ice-flow direction, but rapid in the Bellingshausen Sea. The late Holocene Epoch was characterised by repeated fluctuations in palaeoenvironmental conditions, with associated glacial readvances. However, this has been subsumed by rapid warming and ice-shelf collapse during the twentieth century.

Heuristic based evolution for the coordination of autonomous vehicles in the absence of speed lanes

The current state of the art in the planning and coordination of autonomous vehicles is based upon the presence of speed lanes. In a traffic scenario where there is a large diversity between vehicles the removal of speed lanes can generate a significantly higher traffic bandwidth. Vehicle navigation in such unorganized traffic is considered. An evolutionary based trajectory planning technique has the advantages of making driving efficient and safe, however it also has to surpass the hurdle of computational cost. In this paper, we propose a real time genetic algorithm with Bezier curves for trajectory planning. The main contribution is the integration of vehicle following and overtaking behaviour for general traffic as heuristics for the coordination between vehicles. The resultant coordination strategy is fast and near-optimal. As the vehicles move, uncertainties may arise which are constantly adapted to, and may even lead to either the cancellation of an overtaking procedure or the initiation of one. Higher level planning is performed by Dijkstra's algorithm which indicates the route to be followed by the vehicle in a road network. Re-planning is carried out when a road blockage or obstacle is detected. Experimental results confirm the success of the algorithm subject to optimal high and low-level planning, re-planning and overtaking.

Effects of allometry, productivity and lifestyle on rates and limits of body size evolution

Body size affects nearly all aspects of organismal biology, so it is important to understand the constraints and dynamics of body size evolution. Despite empirical work on the macroevolution and macroecology of minimum and maximum size, there is little general quantitative theory on rates and limits of body size evolution. We present a general theory that integrates individual productivity, the lifestyle component of the slow–fast life-history continuum, and the allometric scaling of generation time to predict a clade's evolutionary rate and asymptotic maximum body size, and the shape of macroevolutionary trajectories during diversifying phases of size evolution. We evaluate this theory using data on the evolution of clade maximum body sizes in mammals during the Cenozoic. As predicted, clade evolutionary rates and asymptotic maximum sizes are larger in more productive clades (e.g. baleen whales), which represent the fast end of the slow–fast lifestyle continuum, and smaller in less productive clades (e.g. primates). The allometric scaling exponent for generation time fundamentally alters the shape of evolutionary trajectories, so allometric effects should be accounted for in models of phenotypic evolution and interpretations of macroevolutionary body size patterns. This work highlights the intimate interplay between the macroecological and macroevolutionary dynamics underlying the generation and maintenance of morphological diversity.

Patterns of maximum body size evolution in Cenozoic land mammals: eco-evolutionary processes and abiotic forcing

There is accumulating evidence that macroevolutionary patterns of mammal evolution during the Cenozoic follow similar trajectories on different continents. This would suggest that such patterns are strongly determined by global abiotic factors, such as climate, or by basic eco-evolutionary processes such as filling of niches by specialization. The similarity of pattern would be expected to extend to the history of individual clades. Here, we investigate the temporal distribution of maximum size observed within individual orders globally and on separate continents. While the maximum size of individual orders of large land mammals show differences and comprise several families, the times at which orders reach their maximum size over time show strong congruence, peaking in the Middle Eocene, the Oligocene and the Plio-Pleistocene. The Eocene peak occurs when global temperature and land mammal diversity are high and is best explained as a result of niche expansion rather than abiotic forcing. Since the Eocene, there is a significant correlation between maximum size frequency and global temperature proxy. The Oligocene peak is not statistically significant and may in part be due to sampling issues. The peak in the Plio-Pleistocene occurs when global temperature and land mammal diversity are low, it is statistically the most robust one and it is best explained by global cooling. We conclude that the macroevolutionary patterns observed are a result of the interplay between eco-evolutionary processes and abiotic forcing

A numerical model of the ionospheric signatures of time-varying magneticreconnection: I. ionospheric convection

This paper presents a numerical model for predicting the evolution of the pattern of ionospheric convection in response to general time-dependent magnetic reconnection at the dayside magnetopause and in the cross-tail current sheet of the geomagnetic tail. The model quantifies the concepts of ionospheric flow excitation by Cowley and Lockwood (1992), assuming a uniform spatial distribution of ionospheric conductivity. The model is demonstrated using an example in which travelling reconnection pulses commence near noon and then move across the dayside magnetopause towards both dawn and dusk. Two such pulses, 8 min apart, are used and each causes the reconnection to be active for 1 min at every MLT that they pass over. This example demonstrates how the convection response to a given change in the interplanetary magnetic field (via the reconnection rate) depends on the previous reconnection history. The causes of this effect are explained. The inherent assumptions and the potential applications of the model are discussed.

JOYCE: Jülich Observatory for cloud evolution

The Jülich Observatory for Cloud Evolution (JOYCE), located at Forschungszentrum Jülich in the most western part of Germany, is a recently established platform for cloud research. The main objective of JOYCE is to provide observations, which improve our understanding of the cloudy boundary layer in a midlatitude environment. Continuous and temporally highly resolved measurements that are specifically suited to characterize the diurnal cycle of water vapor, stability, and turbulence in the lower troposphere are performed with a special focus on atmosphere–surface interaction. In addition, instruments are set up to measure the micro- and macrophysical properties of clouds in detail and how they interact with different boundary layer processes and the large-scale synoptic situation. For this, JOYCE is equipped with an array of state-of-the-art active and passive remote sensing and in situ instruments, which are briefly described in this scientific overview. As an example, a 24-h time series of the evolution of a typical cumulus cloud-topped boundary layer is analyzed with respect to stability, turbulence, and cloud properties. Additionally, we present longer-term statistics, which can be used to elucidate the diurnal cycle of water vapor, drizzle formation through autoconversion, and warm versus cold rain precipitation formation. Both case studies and long-term observations are important for improving the representation of clouds in climate and numerical weather prediction models.

The evolution and heterogeneity of outward foreign direct investment from Latin America

The PhD dissertation investigates the rise of emerging country multinationals (EMNEs), a phenomenon that has opened up a series of research themes and debates. The main debate in this field is the extent to which the theories/frameworks on foreign direct investment (FDI), which have been developed from investigations on multinationals from developed countries, is relevant in explaining outward FDI from EMNEs. This debate is sparked by research suggesting that EMNEs supposedly do not hold the characteristics that are seen as a prerequisite to engaging in FDI. The underlying theme in this PhD is that the field should move away from a one size fit all categorisation of EMNEs, and explore the heterogeneity within EMNEs. Collecting data through various databases, archival articles and annual reports, there was an examination of the internationalisation process of 136 Latin American Multinationals (LAMNEs). The research explores the differences in internationalisation trajectories and global strategies and classifies firms into one of four categories. The four categories that LAMNEs fall into are: Natural-Resource Vertical Integrator, which are firms that are in resource seeking sectors; Accelerated Global, which depict firms that have become global over a very short period of time; Traditional Global, which are EMNEs that have internationalised at the same pace as developed country MNEs and Local Optimisers that only acquire or internationalise to developing countries. The analysis also looks at which decade LAMNEs engaged in FDI, to see if LAMNEs that internationalised during the 1970s and 1980s, during a time when Latin America had a closed economy, was different to LAMNEs that internationalised during the Washington consensus era of the 1990s or to firms that have only just internationalised within the last decade. The findings show that LAMNEs that internationalised before 1990 were more likely to adopt Local Optimiser strategies. However, more LAMNEs that started to internationalise during the 1990s started to adopt Traditional Global strategies, although Local Optimisers were the most prominent strategy. From 2002, there was more prominence of Accelerated Global strategies and a lot more heterogeneity among LAMNEs. Natural-Resource Vertical Integrator LAMNEs, tended to start to internationalisation process during the 1970s/1980s. Despite the rise of EMNEs, and by extension LAMNEs opting to use cross border merger and acquisitions (M&A), there is little research on whether this entry mode has been successful. Contrary to the argument that EMNEs are “internationalising successfully” through this strategy, the findings show that these firms are highly geared and are running less efficiently against their Western competitors. In comparison, LAMNEs internationalising through a more gradual approach, are outperforming their Western competitors on efficiency and are not highly geared- i.e. do not hold a lot of debt. The conclusion of the thesis is the emphasis of moving away from evaluating firms from their country or region of origin, but rather through the global strategy they are using. This will give a more a robust firm level of analysis, and help develop the understanding of EMNEs and international business theory.

Adaptive evolution toward larger size in mammals

The notion that large body size confers some intrinsic advantage to biological species has been debated for centuries. Using a phylogenetic statistical approach that allows the rate of body size evolution to vary across a phylogeny, we find a long-term directional bias toward increasing size in the mammals. This pattern holds separately in 10 of 11 orders for which sufficient data are available and arises from a tendency for accelerated rates of evolution to produce increases, but not decreases, in size. On a branch-by-branch basis, increases in body size have been more than twice as likely as decreases, yielding what amounts to millions and millions of years of rapid and repeated increases in size away from the small ancestral mammal. These results are the first evidence, to our knowledge, from extant species that are compatible with Cope’s rule: the pattern of body size increase through time observed in the mammalian fossil record. We show that this pattern is unlikely to be explained by several nonadaptive mechanisms for increasing size and most likely represents repeated responses to new selective circumstances. By demonstrating that it is possible to uncover ancient evolutionary trends from a combination of a phylogeny and appropriate statistical models, we illustrate how data from extant species can complement paleontological accounts of evolutionary history, opening up new avenues of investigation for both.