Weak Bottlenecks Research Articles

Multiple introductions of divergent lineages and admixture conferred the high invasiveness in a widespread weed (Hypochaeris radicata).

Biological invasion consists of spatially and temporally varying stages, accompanied by ecological and evolutionary changes. Understanding the genomics underlying invasion dynamics provides critical insights into the geographic sources and genetic diversity, contributing to successful invasions across space and time. Here, we used genomic data and model-based approaches to characterize the invasion dynamics of Hypochaeris radicata L., a noxious weed in Korea. Genetic diversity and assignment patterns were investigated using 3563 SNPs of 283 individuals sampled from 22 populations. We employed a coalescent-based simulation method to estimate demographic changes for each population and inferred colonization history using both phylogenetic and population genetic model-based approaches. Our data suggest that H. radicata has been repeatedly been introduced to Korea from multiple genetic sources within the last 50 years, experiencing weak population bottlenecks followed by subsequent population expansions. These findings highlight the potential for further range expansion, particularly in the presence of human-mediated dispersal. Our study represents the first population-level genomic research documenting the invasion dynamics of the successful worldwide invader, H. radicata, outside of Europe.

Global genetic diversity and historical demography of the Bull Shark

AbstractAimBiogeographic boundaries and genetic structuring have important effects on the inferences and interpretation of effective population size (Ne) temporal variations, a key genetics parameter. We reconstructed the historical demography and divergence history of a vulnerable coastal high‐trophic shark using population genomics and assessed our ability to detect recent bottleneck events.LocationWestern and Central Indo‐Pacific (IPA), Western Tropical Atlantic (WTA) and Eastern Tropical Pacific (EPA).TaxonCarcharhinus leucas (Müller & Henle, 1839).MethodsA DArTcap™ approach was used to sequence 475 samples and assess global genetic structuring. Three demographic models were tested on each population, using an ABC‐RF framework coupled with coalescent simulations, to investigate within‐cluster structure. Divergence times between clusters were computed, testing multiple scenarios, with fastsimcoal. Ne temporal variations were reconstructed with STAIRWAYPLOT. Coalescent simulations were performed to determine the detectability of recent bottleneck under the estimated historical trend for datasets of this size.ResultsThree genetic clusters corresponding to the IPA, WTA and EPA regions were identified, agreeing with previous studies. The IPA presented the highest genetic diversity and was consistently identified as the oldest. No significant within‐cluster structuring was detected. Ne increased globally, with an earlier onset in the IPA, during the last glacial period. Coalescent simulations showed that weak and recent bottlenecks could not be detected with our dataset, while old and/or strong bottlenecks would erase the observed ancestral expansion.Main ConclusionsThis study further confirms the role of marine biogeographic breaks in shaping the genetic history of large mobile marine predators. Ne historical increases in Ne are potentially linked to extended coastal habitat availability. The limited within‐cluster population structuring suggests that Ne can be monitored over ocean basins. Due to insufficient amount of available genetic data, it cannot be concluded whether overfishing is impacting Bull Shark genetic diversity, calling for whole‐genome sequencing.

ADA-PC: An asynchronous distributed algorithm for minimizing pairwise connectivity in wireless multi-hop networks

Reliability analysis is of great significance to designing and maintaining wireless multi-hop networks (WMhNs). In WMhNs, several reasons can cause a node to be inoperable, such as hardware failure, software errors, and battery drain. Failure of some critical nodes may partition networks into disconnected segments. The presence of such critical nodes may also reduce the network lifetime since they consume more energy for packet forwarding. Therefore, it is crucial to identify the critical nodes of the networks and strengthen them by adding more nodes surrounding those or creating alternate pathways connecting other nodes to ensure connectivity maintenance in WMhNs. One of the most common approaches in direction is detecting the cut nodes of the networks. However, although finding cut nodes provide helpful information, it may be insufficient for precise reliability analysis since finding cut nodes only does not consider the remaining network. Critical Node Problem (CNP) aims to detect the most important nodes of the network whose removal minimizes the pairwise connectivity (the total number of node pairs connected by at least one path). In other words, the CNP tries to identify a set of nodes whose absence partitions the network into several disconnected segments of similar size. Detecting critical nodes for pairwise connectivity reveals the weak points and bottlenecks of the networks and may help to increase the fault tolerance and lifetime of WMhNs. This paper proposes an Asynchronous Distributed Algorithm for minimizing Pairwise Connectivity (ADA-PC) in WMhNs. To the best of our knowledge, this is the first distributed algorithm for the targeted problem in the network literature. The proposed algorithm uses a distributed Breadth-First Search (BFS) tree which limits bit complexity to O(n.m.log2n) and space complexity to O(d), where d is the network’s diameter. The experimental study on both testbed experiment and simulation reveals that the proposed algorithm is capable of finding the most critical nodes with up to 60% lower sent bytes than the existing central algorithms.

Bottleneck size and selection level reproducibly impact evolution of antibiotic resistance

During antibiotic treatment, the evolution of bacterial pathogens is fundamentally affected by bottlenecks and varying selection levels imposed by the drugs. Bottlenecks—that is, reductions in bacterial population size—lead to an increased influence of random effects (genetic drift) during bacterial evolution, and varying antibiotic concentrations during treatment may favour distinct resistance variants. Both aspects influence the process of bacterial evolution during antibiotic therapy and thereby treatment outcome. Surprisingly, the joint influence of these interconnected factors on the evolution of antibiotic resistance remains largely unexplored. Here we combine evolution experiments with genomic and genetic analyses to demonstrate that bottleneck size and antibiotic-induced selection reproducibly impact the evolutionary path to resistance in pathogenic Pseudomonas aeruginosa, one of the most problematic opportunistic human pathogens. Resistance is favoured—expectedly—under high antibiotic selection and weak bottlenecks, but—unexpectedly—also under low antibiotic selection and severe bottlenecks. The latter is likely to result from a reduced probability of losing favourable variants through drift under weak selection. Moreover, the absence of high resistance under low selection and weak bottlenecks is caused by the spread of low-resistance variants with high competitive fitness under these conditions. We conclude that bottlenecks, in combination with drug-induced selection, are currently neglected key determinants of pathogen evolution and outcome of antibiotic treatment.

Independent domestication events in the blue-cheese fungus Penicillium roqueforti.

Domestication provides an excellent framework for studying adaptive divergence. Using population genomics and phenotypic assays, we reconstructed the domestication history of the blue cheese mould Penicillium roqueforti. We showed that this fungus was domesticated twice independently. The population used in Roquefort originated from an old domestication event associated with weak bottlenecks and exhibited traits beneficial for pre‐industrial cheese production (slower growth in cheese and greater spore production on bread, the traditional multiplication medium). The other cheese population originated more recently from the selection of a single clonal lineage, was associated with all types of blue cheese worldwide except Roquefort, and displayed phenotypes more suited for industrial cheese production (high lipolytic activity, efficient cheese cavity colonization ability and salt tolerance). We detected genomic regions affected by recent positive selection and putative horizontal gene transfers. This study sheds light on the processes of rapid adaptation and raises questions about genetic resource conservation.

Trade Liberalization and Import Intensity in the Mongolian Manufacturing

This article presents an empirical analysis of the consequences of trade liberalization on import intensity in Mongolia, a ‘least-developed landlocked country’ with weak institutions and severe infrastructure bottlenecks. The theoretical framework employed in modelling is based on industrial organization and international trade literature. Our results suggest that foreign investment stimulates import intensity possibly due to the prevalence of intra-firm trade between subsidies, while the protection of domestic market and state ownership reduces import intensity. There is no statistically significant evidence to suggest that import intensity is lower in unskilled labour-intensive industries. These findings have significant policy implications for further liberalization in order to improve Mongolia’s trade competitiveness.

Analyses of Evolutionary Characteristics of the Hemagglutinin-Esterase Gene of Influenza C Virus during a Period of 68 Years Reveals Evolutionary Patterns Different from Influenza A and B Viruses.

Infections with the influenza C virus causing respiratory symptoms are common, particularly among children. Since isolation and detection of the virus are rarely performed, compared with influenza A and B viruses, the small number of available sequences of the virus makes it difficult to analyze its evolutionary dynamics. Recently, we reported the full genome sequence of 102 strains of the virus. Here, we exploited the data to elucidate the evolutionary characteristics and phylodynamics of the virus compared with influenza A and B viruses. Along with our data, we obtained public sequence data of the hemagglutinin-esterase gene of the virus; the dataset consists of 218 unique sequences of the virus collected from 14 countries between 1947 and 2014. Informatics analyses revealed that (1) multiple lineages have been circulating globally; (2) there have been weak and infrequent selective bottlenecks; (3) the evolutionary rate is low because of weak positive selection and a low capability to induce mutations; and (4) there is no significant positive selection although a few mutations affecting its antigenicity have been induced. The unique evolutionary dynamics of the influenza C virus must be shaped by multiple factors, including virological, immunological, and epidemiological characteristics.

3D Microstructure Effects in Ni-YSZ Anodes: Influence of TPB Lengths on the Electrochemical Performance

3D microstructure-performance relationships in Ni-YSZ anodes for electrolyte-supported cells are investigated in terms of the correlation between the triple phase boundary (TPB) length and polarization resistance (Rpol). Three different Ni-YSZ anodes of varying microstructure are subjected to eight reduction-oxidation (redox) cycles at 950 °C. In general the TPB lengths correlate with anode performance. However, the quantitative results also show that there is no simplistic relationship between TPB and Rpol. The degradation mechanism strongly depends on the initial microstructure. Finer microstructures exhibit lower degradation rates of TPB and Rpol. In fine microstructures, TPB loss is found to be due to Ni coarsening, while in coarse microstructures reduction of active TPB results mainly from loss of YSZ percolation. The latter is attributed to weak bottlenecks associated with lower sintering activity of the coarse YSZ. The coarse anode suffers from complete loss of YSZ connectivity and associated drop of TPBactive by 93%. Surprisingly, this severe microstructure degradation did not lead to electrochemical failure. Mechanistic scenarios are discussed for different anode microstructures. These scenarios are based on a model for coupled charge transfer and transport, which allows using TPB and effective properties as input. The mechanistic scenarios describe the microstructure influence on current distributions, which explains the observed complex relationship between TPB lengths and anode performances. The observed loss of YSZ percolation in the coarse anode is not detrimental because the electrochemical activity is concentrated in a narrow active layer. The anode performance can be predicted reliably if the volume-averaged properties (TPBactive, effective ionic conductivity) are corrected for the so-called short-range effect, which is particularly important in cases with a narrow active layer.

Simulation Techniques in Public Administration Procedures

Public administration is undergoing a series of reforms. These influence the management methods and techniques originating in the private sector in the management’s everyday work. With the intention to gain a more transparent overview of the administrative processes and to make them more transparent and manageable, the simulation methods are being implemented. They expose the weak points and bottlenecks of the organisation. The article describes the problems of collecting the data on elementary operations. The documentation databases have been analysed with the aim to define the elapsed time for a single administrative operation and the probability of transformation of a transaction from one process state to another. The article presents the experience gained in the implementation of the Micrografx iGrafx Process 2000 as a simulation tool. It also provides a practical example of simulation of an administrative process by means of the above-mentioned tool.

What Happened to Gray Whales during the Pleistocene? The Ecological Impact of Sea-Level Change on Benthic Feeding Areas in the North Pacific Ocean

BackgroundGray whales (Eschrichtius robustus) undertake long migrations, from Baja California to Alaska, to feed on seasonally productive benthos of the Bering and Chukchi seas. The invertebrates that form their primary prey are restricted to shallow water environments, but global sea-level changes during the Pleistocene eliminated or reduced this critical habitat multiple times. Because the fossil record of gray whales is coincident with the onset of Northern Hemisphere glaciation, gray whales survived these massive changes to their feeding habitat, but it is unclear how.Methodology/Principal FindingsWe reconstructed gray whale carrying capacity fluctuations during the past 120,000 years by quantifying gray whale feeding habitat availability using bathymetric data for the North Pacific Ocean, constrained by their maximum diving depth. We calculated carrying capacity based on modern estimates of metabolic demand, prey availability, and feeding duration; we also constrained our estimates to reflect current population size and account for glaciated and non-glaciated areas in the North Pacific. Our results show that key feeding areas eliminated by sea-level lowstands were not replaced by commensurate areas. Our reconstructions show that such reductions affected carrying capacity, and harmonic means of these fluctuations do not differ dramatically from genetic estimates of carrying capacity.Conclusions/SignificanceAssuming current carrying capacity estimates, Pleistocene glacial maxima may have created multiple, weak genetic bottlenecks, although the current temporal resolution of genetic datasets does not test for such signals. Our results do not, however, falsify molecular estimates of pre-whaling population size because those abundances would have been sufficient to survive the loss of major benthic feeding areas (i.e., the majority of the Bering Shelf) during glacial maxima. We propose that gray whales survived the disappearance of their primary feeding ground by employing generalist filter-feeding modes, similar to the resident gray whales found between northern Washington State and Vancouver Island.

An assessment of genetic diversity in wild and captive populations of endangered Japanese bitterling Tanakia tanago (Cyprinidae) using amplified fragment length polymorphism (AFLP) markers

The Japanese bitterling Tanakia tanago (Cyprinidae) is on the verge of extinction in the wild, placing great importance on captive breeding programs for current conservation of the species. However, the loss of genetic diversity during captive breeding is an ongoing matter of concern. Since some captive populations have been almost monomorphic in mitochondrial DNA (mtDNA), this hampers assessments of their genetic diversity during captive breeding. To more accurately assess their genetic diversity, one wild and three captive populations were examined using amplified fragment length polymorphism (AFLP) markers. Estimates of average heterozygosity and nucleotide diversity ranged 0.0479–0.1920 and 0.0023–0.0088, respectively, enabling comparison of genetic diversity among the wild and captive populations, and among year-classes of captive populations. Significant differences in numbers of amplified fragments and proportions of polymorphic fragments were observed among year-classes of all populations. The indices of genetic diversity calculated from AFLP seemed to be, however, less sensitive to weak bottlenecks. No continuous decrease in genetic diversity in nuclear DNA was detected in presently captive populations. This supports the possibility of re-introduction of the captive populations into the original habitats, although survival and reproductive ability in the wild must be taken into consideration.

A multi-scale approach in the study of plant regeneration: Finding bottlenecks is not enough

Using a multi-scale design, we investigated the spatio-temporal variability and concordance across recruitment stages of the Mediterranean fleshy-fruited shrub Daphne gnidium. The patterns of seed rain, post-dispersal seed predation, seedling emergence, survival and growth were studied in two populations in contrasting conditions, in an olive grove and in a dune system, in Mallorca (Balearic Islands) during two consecutive seasons. We considered 20 sites (fine scale) in four microhabitats (medium scale) in each population (large scale). Most seeds were dropped under parent plants, especially in the population with presumably less seed dispersers. Post-dispersal seed predation (ca. 90%) represented the most important bottleneck in plant recruitment in all microhabitats at both populations. Seedling emergence was also similar at both populations although seedling survival was higher in the olive grove. One year after of emergence, seedlings under shrubs were taller – though not necessarily had more leaves – than in the other microhabitats. There was a positive and consistent effect of seed size across microhabitats on seedling emergence, survival and growth (maximum length) although its intensity varied between populations and years. Concordance between seed rain and seedling recruitment was affected by the heterogeneity of population-dependent forces acting upon each recruitment stage. There were stages, which represented a strong bottleneck but were little discordant with seed rain. By contrast, other weak bottlenecks were hardly discordant with seed rain. Our study stresses the importance of considering simultaneously the critical stages (i.e., bottlenecks) and the concordance between seed dispersal and post-dispersal stages in plant recruitment studies.

Does Number of Beds Reflect the Surgical Capability of Hospitals in Wartime and Disaster? The Use of a Simulation Technique at a National Level

The raw number of hospital trauma beds and occupancy has been used to assess the surgical capability of hospitals in wartime and disaster situations. The goal of this study was to examine and offer a better tool to determine the load of casualties that a hospital would be able to absorb and treat effectively during these situations. Simulation software was applied to various wartime scenarios. It assessed the usefulness of a computerized simulation of operating room (OR) function under loading of "standard wartime casualties." Comparison of the functioning of similar hospitals was undertaken in order to identify possible methods to optimize the care delivered. A "what-if" module was used to define the optimal way to absorb mass casualties within the known resources of a given healthcare system. Each hospital was tested under different loading of "standard casualties." Average waiting time for surgery was used as a marker of the constant decay in the standards of care with the increasing patient load. Different, unique patterns of strategies for optimizing waiting periods were identified. Not all trauma centers responded by shortening waiting time by diverting the lightly injured patients from them either before or after triage. The reaction to alternate days' shift was unexpected. The temporal course of matching a patient with a functional operating room was more indicative of a hospital's capability to absorb casualties requiring surgery than was the pre-set number of beds available in the hospital. The use of simulation techniques might be useful method to assess the nationwide surgical capability. This is a complex dilemma that cannot be predicted with trivial guessing, even when combined with previous experience of triaging. Analyzing the weak points and bottlenecks at a national level might help in creating preparedness protocols.

Catching Speeding Electrons in a Circuit City

MICROELECTRONICS T ake a long-exposure aerial photograph of a city at night, and you will see traffic patterns traced in the bright streams and dense clusters of car headlights. The image (below), obtained by a team of researchers at the IBM Thomas J. Watson Research Center in Yorktown Heights, New York, is the equivalent shot of a functioning microprocessor, the 1997 S/390 used in the current generation of IBM mainframes. The “traffic” consists of electrons emitting light as they pass through the transistors, or crossroads, of this silicon city. By directly viewing such traffic patterns, circuit designers can look for weak spots and bottlenecks in the millions of components on a chip. ![Figure][1] IBM “Researchers have known since the 1980s that electrons emit light as they pass through the field-effect transistors [FETs] at the heart of most modern microchips,” says Jeffrey Kash, of the IBM team that made the images. The light, which is in the near infrared and is extremely weak, can be detected only with cooled charge-coupled devices or special photomultiplier imaging tubes. Kash and his colleague James Tsang investigated this particular microprocessor because it consumed two orders of magnitude more current than it should have when it was not performing any operations. Kash and his colleagues obtained images of the chip in this “quiescent” state that showed a series of spots indicating that this excessive current was confined to a small portion of the chip. They couldn't tell which of the 7.8 million transistors were at fault, however, because they couldn't identify individual transistors in their images. “The issue was, how do you know where you are, how do you navigate,” says Kash. The team solved the navigation problem by spying on the individual FETs as they shuttled electrons around the chip when it was operating normally. “The only time a current is flowing is when you have a change of logic state,” says Kash. The FETs produce picosecond light pulses as they switch on and off, so by photographing the chip in normal operation, Kash and his colleagues obtained a “road map” of the positions of the FETs. When the researchers superimposed this image on the photo showing the excess leak currents, they pinpointed exactly where the leaks occur. The technique is useful for more than troubleshooting. “We can look at hundreds of thousands of FETs on a chip,” says Kash, “and that is very helpful” in improving the design of subsequent chips. Indeed, Ingrid De Wolf of IMEC, Belgium's Interuniversity Microelectronics Center in Leuven, says optical-emission diagnosis of chips is beginning to spread throughout the microelectronics industry. Researchers are going beyond simple imaging, she adds: “We are now also trying to get more information from the spectrum of the emitted light, so we can measure the energy of the electrons.” [1]: pending:yes

Freight Components in Louisiana's Statewide Intermodal Transportation Plan

Planning procedures used in addressing freight components for Louisiana's statewide intermodal transportation plan are described. The effort was unprecedented in Louisiana, and the experience can be applied in other states. User and provider involvement, demand analysis, network analysis, and recommended policies and programs for the water, rail, and intermodal freight components are described. Although an assessment of system capacity remained at the core of the effort, low cost improvements in system performance were also addressed. Analysis of future demand for facility capacity was performed in three steps. First, baseline historical flow patterns, including volume and modal orientation of inbound, outbound, intrastate, and transhipped movements, were established through extensive processing of data obtained. Second, volume forecasts for 11 major commodity groups were made for each of three possible growth scenarios. Third, a strategic outlook was developed for selected commodity types to examine market structure, productivity trends, and the competitive position of transportation providers in the state. Network capacity analysis identified few weak links or bottlenecks in the state's main line waterway and railroad networks. A stock and flow approach was taken to measure the capacity of various types of cargo transfer terminals. A comparative analysis of maritime terminal productivity and cost was performed to assess the competitiveness of ports in Louisiana. An extensive survey of the physical, operating, and institutional characteristics of terminal roadway and railroad access links was made.

Freight Components in Louisiana's Statewide Intermodal Transportation Plan

Planning procedures used in addressing freight components for Louisiana's statewide intermodal transportation plan are described. The effort was unprecedented in Louisiana, and the experience can be applied in other states. User and provider involvement, demand analysis, network analysis, and recommended policies and programs for the water, rail, and intermodal freight components are described. Although an assessment of system capacity remained at the core of the effort, low cost improvements in system performance were also addressed. Analysis of future demand for facility capacity was performed in three steps. First, baseline historical flow patterns, including volume and modal orientation of inbound, outbound, intrastate, and transhipped movements, were established through extensive processing of data obtained. Second, volume forecasts for 11 major commodity groups were made for each of three possible growth scenarios. Third, a strategic outlook was developed for selected commodity types to examine market structure, productivity trends, and the competitive position of transportation providers in the state. Network capacity analysis identified few weak links or bottlenecks in the state's main line waterway and railroad networks. A stock and flow approach was taken to measure the capacity of various types of cargo transfer terminals. A comparative analysis of maritime terminal productivity and cost was performed to assess the competitiveness of ports in Louisiana. An extensive survey of the physical, operating, and institutional characteristics of terminal roadway and railroad access links was made.

Optical spectra and kinetics of single impurity molecules in a polymer: spectral diffusion and persistent spectral hole burning

With high-efficiency fluorescence excitation techniques optical spectra of single impurity molecules of perylene in a polyethylene matrix can be obtained at 1.5 K. Analysis of such spectra shows a variety of spectral diffusion effects, including fast (<2 s) resonance frequency changes on the 1–100-MHz scale, which lead to a range of apparent linewidths, as well as discontinuous jumps in the resonance frequency of 10–1000 MHz on a longer time scale. In addition, light-induced changes in the resonance frequency of a single molecule (persistent spectral hole burning) have been conclusively observed by showing that the burning time decreases with increased laser power. Surprisingly, hole-burned single molecules often spontaneously return to the original frequency in 1–100 s. Measurements of the burning time for a large number of hole-burning events for the same single molecule yield an exponential burn-time distribution, which is the first direct measurement to our knowledge of the stochastic kinetics of a single molecule. Analysis of the signal-to-noise function appropriate to these experiments gives the conditions under which other systems may permit single-molecule detection: strong absorption, high fluorescence yield, weak bottlenecks in the optical pumping process, and low hole-burning quantum efficiency.