Severe Bottleneck Research Articles

Assessing the genetic diversity and population structure of the endangered Chascolytrum bulbosum (Poaceae, Poeae) using AFLP markers

Chascolytrum bulbosum occurs in shrubby fields with granite outcrops in southern South America. It is considered endangered, due to habitat loss and overgrazing. However, no population genetic studies nor conservation management plan for the species is currently available. Therefore, Amplified Fragment Length Polymorphism (AFLP) markers were used to assess genetic diversity and infer population structure of 13 natural populations of C. bulbosum distributed across southern Brazil. A total of 651 AFLP fragments were produced, of which 98.2% were polymorphic. Genetic diversity was considered moderate (H = 0.150), with genetic differentiation being moderate to high (GST = 0.228; FST = 0.341). Analyses enabled the separation of individuals into two clusters, although AMOVA results suggest only 13.2% variation between them. Estimates of gene flow by migration (Nm) were high in all analyses. Results suggest that no severe bottleneck has occurred recently in populations analyzed in this study. As gene flow occurs broadly through the geographical range of species found in Rio Grande do Sul, we suggest the stimulation of in situ rather than ex situ conservation, and priority populations for conservation of C. bulbosum are indicated.

Adaptation in isolated populations: when does it happen and when can we tell?

Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here, we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affect the ability of outlier scans for selection to identify adaptive alleles using both single-site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur and yet the adaptive variants are most likely to derive from a single ancestor (a 'hard' selective sweep); in this zone, four commonly used statistics detect selection with high power. Real-world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole-genome sequencing of differentiated populations.

An Ontological Approach for Originating Data Services with Hazy Semantics

Objective: The tremendous growth in volume of data is increasing the complexity of data handling. The existing content based search is not only complex and expensive, but also leads to poor processing and unacceptable latency for massive amount of data. Data accessed from large dataset using existing approach will slow down the query response rate. High resource cost is the severe performance bottleneck caused by query operations. The semantic based search can be carried out on the data, In order to reduce the complexity in data handling. The proposed method uses Resource Description Framework (RDF) with Ontology Web Language (OWL). Thus the RDF is used for non domain based search and OWL is used for domain based search. The non domain based search provides the composition of best data services from master RDF. The triplets from different RDF are combined to form master RDF. And the domain based search is one which provides recommendations for the user based on their search query. The main objective of this approach is to provide semantic search using RDF and recommendation using OWL. The search result will be the high similarity result sets as the method uses the combinational RDF to form large master RDF. Statistical Analysis/Methods: The user is provided with two methods of searching which is domain based search and non domain based search. The domain based search is one which provides recommendation for the user based on the search query. And the non domain based search originates the data services from master RDF. Agriculture data set is chosen as a sample data set for domain based search which can be extended further for any other domain. The web services which contain general information about the world and also related web services is chosen as a data set for non domain based search. Findings: The statistical analysis of ontology based semantic search with keyword based search produced the precision value of 0.8 out of 1.0 using the search results obtained from both semantic search and keyword based search. Applications/Improvements: The application can be further improved by adding realistic data sets and increasing the size of the database. The domain based approach is not restricted only to agriculture but it can also be extended to some other applications like Health care, pattern recognition and so on.

Crop domestication facilitated rapid geographical expansion of a specialist pollinator, the squash bee Peponapis pruinosa.

Squash was first domesticated in Mexico and is now found throughout North America (NA) along with Peponapis pruinosa, a pollen specialist bee species of the squash genus Cucurbita The origin and spread of squash cultivation is well-studied archaeologically and phylogenetically; however, no study has documented how cultivation of this or any other crop has influenced species in mutualistic interactions. We used molecular markers to reconstruct the demographic range expansion and colonization routes of P. pruinosa from its native range into temperate NA. Populations east of the Rocky Mountains expanded from the wild host plant's range in Mexico and were established by a series of founder events. Eastern North America was most likely colonized from squash bee populations in the present-day continental Midwest USA and not from routes that followed the Gulf and Atlantic coasts from Mexico. Populations of P. pruinosa west of the Rockies spread north from the warm deserts much more recently, showing two genetically differentiated populations with no admixture: one in California and the other one in eastern Great Basin. These bees have repeatedly endured severe bottlenecks as they colonized NA, following human spread of their Cucurbita pollen hosts during the Holocene.

Inbreeding and Mortality Risk in a Captive Population of Mhorr Gazelle (Nanger dama mhorr)

This study aimed to evaluate the genetic variation and examine the association of inbreeding level on mortality risk (at days 7, 30 and 180 – weaning age) of Mhorr gazelle in captivity for the year 1969–2000 as recorded in the studbook record kept by Australasian Regional Association of Zoological Parks and Aquaria (ARAZPA). The effective number of founders, ancestors and founder genomes was found to be 3.42, 3, and 1.44 for the studied reference population. The reference population is composed of animals which are alive, with known parents and known sex. Animals that are less than 10 years old (based on birth dates up to 2008) with no remarks on its death are considered alive. The population may not have experienced a severe bottleneck, as the values on the effective number of founders and ancestors are almost equal. However, the effective number of founder genomes is low, which demonstrates gene loss due to genetic drift. The mean inbreeding coefficients of the individual, sire and dam were found to be 0.2971 ± 0.1043, 0.2300 ± 0.1141 0.2339 ± 0.1070, respectively. The maximum inbreeding level of the population is 0.5247 (52.47%). This means that parent–offspring or full-sib mating must have happened. The increase in inbreeding level of an individual was found to be significantly associated (p<0.10) with an increase in p mortality risk at day 180 or weaning age. Increasing inbreeding level of sires was found to be significantly associated with increasing risk in mortality at day 30, which indicates that inbred parents also can influence the survival of an offspring. Efficient breeding programs are as important for decreasing mortality in captive populations, as the provision of optimum zoo management practices.

Decentralized Thermal-Aware Task Scheduling for Large-Scale Many-Core Systems

Technology scaling has enabled fast increase in the number of cores integrated in many-core systems. However, feature size shrinking also makes large-scale many-core systems vulnerable to thermal failures. Thermal-aware task scheduling is an efficient technique to reduce the run-time temperatures of many-core processors. Most existing thermal-aware task scheduling algorithms leverage centralized scheduling schemes to gather the overall information and generate the task schedule at a center scheduler. Although that scheme can achieve the optimal temperature reduction, however, it faces severe computation bottleneck and communication congestion when the many-core processors evolve to large-scale with hundreds or thousands of cores. In this paper, we propose a decentralized thermal-aware scheduling algorithm to address this problem in large-scale systems. Experiment results on various benchmarks show that our decentralized algorithm achieves significant improvement on scalability (up to 84.3% reduction in monitoring traffic) and similar benefits on temperature reduction (by 5%) when compared with the state-of-the-art thermal-aware scheduling algorithm.

Multiperspective Focus+Context Visualization.

Occlusions are a severe bottleneck for the visualization of large and complex datasets. Conventional images only show dataset elements to which there is a direct line of sight, which significantly limits the information bandwidth of the visualization. Multiperspective visualization is a powerful approach for alleviating occlusions to show more than what is visible from a single viewpoint. However, constructing and rendering multiperspective visualizations is challenging. We present a framework for designing multiperspective focus+context visualizations with great flexibility by manipulating the underlying camera model. The focus region viewpoint is adapted to alleviate occlusions. The framework supports multiperspective visualization in three scenarios. In a first scenario, the viewpoint is altered independently for individual image regions to avoid occlusions. In a second scenario, conventional input images are connected into a multiperspective image. In a third scenario, one or several data subsets of interest (i.e., targets) are visualized where they would be seen in the absence of occluders, as the user navigates or the targets move. The multiperspective images are rendered at interactive rates, leveraging the camera model's fast projection operation. We demonstrate the framework on terrain, urban, and molecular biology geometric datasets, as well as on volume rendered density datasets.

Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China.

Climate oscillations are the key factors to understand the patterns in modern biodiversity. East Asia harbors the most diverse temperate flora, largely because an extensive terrestrial ice cap was absent during repeated Pleistocene glaciation–interglacial cycles. Comparing the demographic histories of species that are codistributed and are close relatives may provide insight into how the process of climate change influences species ranges. In this study, we compared the spatial genetic structure and demographic histories of two coexisting Eleutherococcus species, Eleutherococcus senticosus and E. sessiliflorus. Both species are distributed in northern China, regions that are generally considered to be sensitive to climatic fluctuations. These regions once hosted temperate forest, but this temperate forest was replaced by tundra and taiga forest during the Last Glacial Maximum (LGM), according to pollen records. Using three chloroplast DNA fragments, we assessed the genetic structure of 20 and 9 natural populations of E. senticosus and E. sessiliflorus, respectively. Extremely contrasting genetic patterns were found between the two species; E. sessiliflorus had little genetic variation, whereas E. senticosus had considerably higher levels of genetic variation (15 haplotypes). We speculated that a recent severe bottleneck may have resulted in the extremely low genetic diversity in E. sessiliflorus. In E. senticosus, populations in Northeast China (NEC) harbored all of the haplotypes found in this species and included private haplotypes. The populations in NEC had higher levels of genetic diversity than did those from North China (NC). Therefore, we suggest that both the NC and NEC regions can sustain LGM refugia and that lineage admixture from multiple refugia took place after the LGM elevated the local genetic diversity in NEC. In NEC, multiple genetic hot spots were found in the Changbai Mountains and the Xiaoxing'an Range, which implied that multiple locations in NEC may sustain LGM refugia, even in the Xiaoxing'an Range.

The history of Old World camelids in the light of molecular genetics.

Old World camels have come into the focus as sustainable livestock species, unique in their morphological and physiological characteristics and capable of providing vital products even under extreme environmental conditions. The evolutionary history of dromedary and Bactrian camels traces back to the middle Eocene (around 40 million years ago, mya), when the ancestors of Camelus emerged on the North American continent. While the genetic status of the two domestic species has long been established, the wild two-humped camel has only recently been recognized as a separate species, Camelus ferus, based on molecular genetic data. The demographic history established from genome drafts of Old World camels shows the independent development of the three species over the last 100,000 years with severe bottlenecks occurring during the last glacial period and in the recent past. Ongoing studies involve the immune system, relevant production traits, and the global population structure and domestication of Old World camels. Based on the now available whole genome drafts, specific metabolic pathways have been described shedding new light on the camels’ ability to adapt to desert environments. These new data will also be at the origin for genome-wide association studies to link economically relevant phenotypes to genotypes and to conserve the diverse genetic resources in Old World camelids.

Imprints of multiple glacial refugia in the Pyrenees revealed by phylogeography and palaeodistribution modelling of an endemic spider.

Mediterranean mountain ranges harbour highly endemic biota in islandlike habitats. Their topographic diversity offered the opportunity for mountain species to persist in refugial areas during episodes of major climatic change. We investigate the role of Quaternary climatic oscillations in shaping the demographic history and distribution ranges in the spider Harpactocrates ravastellus, endemic to the Pyrenees. Gene trees and multispecies coalescent analyses on mitochondrial and nuclear DNA sequences unveiled two distinct lineages with a hybrid zone around the northwestern area of the Catalan Pyrenees. The lineages were further supported by morphological differences. Climatic niche-based species distribution models (SDMs) identified two lowland refugia at the western and eastern extremes of the mountain range, which would suggest secondary contact following postglacial expansion of populations from both refugia. Neutrality test and approximate Bayesian computation (ABC) analyses indicated that several local populations underwent severe bottlenecks followed by population expansions, which in combination with the deep population differentiation provided evidence for population survival during glacial periods in microrefugia across the mountain range, in addition to the main Atlantic and Mediterranean (western and eastern) refugia. This study sheds light on the complexities of Quaternary climatic oscillations in building up genetic diversity and local endemicity in the southern Europe mountain ranges.

Building Heterogeneous Unified Virtual Memories (UVMs) without the Overhead

This work proposes a novel scheme to facilitate heterogeneous systems with unified virtual memory. Research proposals implement coherence protocols for sequential consistency (SC) between central processing unit (CPU) cores and between devices. Such mechanisms introduce severe bottlenecks in the system; therefore, we adopt the heterogeneous-race-free (HRF) memory model. The use of HRF simplifies the coherency protocol and the graphics processing unit (GPU) memory management unit (MMU). Our protocol optimizes CPU and GPU demands separately, with the GPU part being simpler while the CPU is more elaborate and latency aware. We achieve an average 45% speedup and 45% energy-delay product reduction (20% energy) over the corresponding SC implementation.

Large-scale mitogenomics enables insights into Schizophora (Diptera) radiation and population diversity.

True flies are insects of the order Diptera and encompass one of the most diverse groups of animals on Earth. Within dipterans, Schizophora represents a recent radiation of insects that was used as a model to develop a pipeline for generating complete mitogenomes using various sequencing platforms and strategies. 91 mitogenomes from 32 different species were sequenced and assembled with high fidelity, using amplicon, whole genome shotgun or single molecule sequencing approaches. Based on the novel mitogenomes, we estimate the origin of Schizophora within the Cretaceous-Paleogene (K-Pg) boundary, about 68.3 Ma. Detailed analyses of the blowfly family (Calliphoridae) place its origin at 22 Ma, concomitant with the radiation of grazing mammals. The emergence of ectoparasitism within calliphorids was dated 6.95 Ma for the screwworm fly and 2.3 Ma for the Australian sheep blowfly. Varying population histories were observed for the blowfly Chrysomya megacephala and the housefly Musca domestica samples in our dataset. Whereas blowflies (n = 50) appear to have undergone selective sweeps and/or severe bottlenecks in the New World, houseflies (n = 14) display variation among populations from different zoogeographical zones and low levels of gene flow. The reported high-throughput mitogenomics approach for insects enables new insights into schizophoran diversity and population history of flies.

Genetic variation in a freshwater prawn species, Palaemon paucidens, in South Korea

The biogeography of freshwater biota in the Korean Peninsula has been affected by recent geological processes and anthropogenic activity. The freshwater prawn, Palaemon paucidens, can serve as a non-fish model organism suitable for assessing these factors, as it is found in all river systems in the Korean Peninsula and may have been introduced by humans in some regions. In this study, we investigated the geographical distribution of genetic variation and the genetic structure of P. paucidens populations using mitochondrial DNA sequences and genotypes identified from four microsatellite loci. Our results showed that populations from westward-flowing river systems that drain into the Yellow Sea have more genetic diversity than those from southward-flowing river systems, and that the highest genetic variance revealed by analysis of molecular variance (AMOVA) using both genetic markers was observed in river systems grouped as HAN + GEUM, NAKDONG + JEJU, YOUNGSAN, and SEOMJIN. These results suggest that HAN and GEUM, in which freshwater prawn populations have higher levels of genetic diversity, were the most recently isolated river systems from Asian continental systems. Therefore, populations from HAN and GEUM experienced less severe bottlenecks than those from YOUNGSAN and SEOMJIN.

Efficient Temperature-Dependent Green's Functions Methods for Realistic Systems: Compact Grids for Orthogonal Polynomial Transforms.

The Matsubara Green's function that is used to describe temperature-dependent behavior is expressed on a numerical grid. While such a grid usually has a couple of hundred points for low-energy model systems, for realistic systems with large basis sets the size of an accurate grid can be tens of thousands of points, constituting a severe computational and memory bottleneck. In this paper, we determine efficient imaginary time grids for the temperature-dependent Matsubara Green's function formalism that can be used for calculations on realistic systems. We show that, because of the use of an orthogonal polynomial transform, we can restrict the imaginary time grid to a few hundred points and reach micro-Hartree accuracy in the electronic energy evaluation. Moreover, we show that only a limited number of orthogonal polynomial expansion coefficients are necessary to preserve accuracy when working with a dual representation of the Green's function or self-energy and transforming between the imaginary time and frequency domain.

Ancient DNA reveals substantial genetic diversity in the California Condor (Gymnogyps californianus) prior to a population bottleneck

ABSTRACT Critically endangered species that have undergone severe population bottlenecks often have little remaining genetic variation, making it difficult to reconstruct population histories to apply in reintroduction and recovery strategies. By using ancient DNA techniques, it is possible to combine genetic evidence from the historical population with contemporary samples to provide a more complete picture of a species' genetic variation across its historical range and through time. Applying this approach, we examined changes in the mitochondrial DNA (mtDNA) control region (526 base pairs) of the endangered California Condor (Gymnogyps californianus). Results showed a >80% reduction in unique haplotypes over the past 2 centuries. We found no spatial sorting of haplotypes in the historical population; the periphery of the range contained haplotypes that were common throughout the historical range. Direct examination of mtDNA from California Condor museum specimens provided a new window into historical po...

Demographic history of Trinorchestia longiramus (Amphipoda, Talitridae) in South Korea inferred from mitochondrial DNA sequence variation

We investigated the demographic history ofTrinorchestia longiramusJo, 1988 using the nucleotide sequence analysis of the mitochondrial cytochrome oxidase subunit I (COI) gene from 277 individuals collected from eight Korean populations. From the low haplotype diversity and nucleotide diversity in all populations, a neutrality test, and mismatch distribution analysis, the species appears to have recently experienced a prolonged or severe demographic bottleneck. Pairwise populationFSTestimates and AMOVA [= Analysis of Molecular Variance] results showed that substantial differentiation is present between the southern and eastern populations. The population structure ofT. longiramusmay have been influenced by glacial population extinctions and interglacial colonization during the Pleistocene ice-ages.

1.5 Gbit/s FPGA Implementation of a Fully-Parallel Turbo Decoder Designed for Mission-Critical Machine-Type Communication Applications

In wireless communication schemes, turbo codes facilitate near-capacity transmission throughputs by achieving reliable forward error correction. However, owing to the serial data dependencies imposed by the underlying logarithmic Bahl–Cocke-Jelinek–Raviv (Log-BCJR) algorithm, the limited processing throughputs of conventional turbo decoder implementations impose a severe bottleneck upon the overall throughputs of real-time wireless communication schemes. Motivated by this, we recently proposed a fully parallel turbo decoder (FPTD) algorithm, which eliminates these serial data dependencies, allowing parallel processing and hence offering a significantly higher processing throughput. In this paper, we propose a novel resource-efficient version of the FPTD algorithm, which reduces its computational resource requirement by 50%, which enhancing its suitability for field-programmable gate array (FPGA) implementations. We propose a model FPGA implementation. When using a Stratix IV FPGA, the proposed FPTD FPGA implementation achieves an average throughput of 1.53 Gb/s and an average latency of 0.56 $\mu \text{s}$ , when decoding frames comprising ${N}=720$ b. These are, respectively, 13.2 times and 11.1 times superior to those of the state-of-the-art FPGA implementation of the Log-BCJR long-term evolution (LTE) turbo decoder, when decoding frames of the same frame length at the same error correction capability. Furthermore, our proposed FPTD FPGA implementation achieves a normalized resource usage of 0.42 (kALUTs/Mb/s), which is 5.2 times superior to that of the benchmarker decoder. Furthermore, when decoding the shortest $N=40$ -b LTE frames, the proposed FPTD FPGA implementation achieves an average throughput of 442 Mb/s and an average latency of 0.18 $\mu \text{s}$ , which are, respectively, 21.1 times and 10.6 times superior to those of the benchmarker decoder. In this case, the normalized resource usage of 0.08 (kALUTs/Mb/s) is 146.4 times superior to that of the benchmarker decoder.

Capturing the Benefits of a Variable Advisory Speed System in Portland, Oregon: Empirical Before and After Evaluation

The first variable advisory speed (VAS) system in Portland, Oregon, was recently installed on OR-217. This system, designed to be responsive to both congestion and weather, was installed to address issues along the corridor, including unreliable travel times, high crash rates, and substantial declines in performance during adverse weather. To assess the merits and effectiveness of the VAS system, a before and after analysis of corridor performance in terms of capacity, reliability, and safety is being conducted. This paper summarizes the findings of the before analysis and presents results from the after analysis during the first 9 months of operation. Before the system’s activation, OR-217 suffered from highly variable travel times, frequent severe bottlenecks, a high rate of rear-end collisions, and significant speed differentials between adjacent lanes. Though the system was activated in the summer of 2014 and the system’s long-term effects are not yet definitely established, some notable evidence of travel time reliability improvements has already been documented. The system’s safety impacts will be the subject of ongoing analysis.

VLSI Implementation of Fully Parallel LTE Turbo Decoders

Turbo codes facilitate near-capacity transmission throughputs by achieving a reliable iterative forward error correction. However, owing to the serial data dependence imposed by the logarithmic Bahl–Cocke–Jelinek–Raviv algorithm, the limited processing throughputs of the conventional turbo decoder implementations impose a severe bottleneck upon the overall throughputs of real-time communication schemes. Motivated by this, we recently proposed a floating-point fully parallel turbo decoder (FPTD) algorithm, which eliminates the serial data dependence, allowing parallel processing and hence significantly reducing the number of clock cycles required. In this paper, we conceive a technique for reducing the critical datapath of the FPTD, and we propose a novel fixed-point version as well as its very large scale integration (VLSI) implementation. We also propose a novel technique, which allows the FPTD to also decode shorter frames employing compatible interleaver patterns. We strike beneficial tradeoffs amongst the latency, core area, and energy consumption by investigating the minimum bit widths and techniques for message log-likelihood ratio scaling and state metric normalization. Accordingly, the design flow and design tradeoffs considered in this paper are also applicable to other fixed-point implementations of error correction decoders. We demonstrate that upon using Taiwan Semiconductor Manufacturing Company (TSMC) 65-nm low-power technology for decoding the longest long-term evolution frames (6144 b) received over an additive white Gaussian noise channel having $E_{b}/N_{0}=1~ \text {dB}$ , the proposed fixed-point FPTD VLSI achieves a processing throughput of 21.9 Gb/s and a processing latency of $0.28~ \mu \text {s}$ . These results are 17.1 times superior to those of the state-of-the-art benchmarker. Furthermore, the proposed fixed-point FPTD VLSI achieves an energy consumption of $2.69~ \mu \text {J}$ /frame and a normalized core area of $5~ \text {mm}^{\vphantom {R^{'}}2}/\text {Gb/s}$ , which are 34% and 23% lower than those of the benchmarker, respectively.

Looking into the past - the reaction of three grouse species to climate change over the last million years using whole genome sequences.

Tracking past population fluctuations can give insight into current levels of genetic variation present within species. Analysing population dynamics over larger timescales can be aligned to known climatic changes to determine the response of species to varying environments. Here, we applied the Pairwise Sequentially Markovian Coalescent (psmc) model to infer past population dynamics of three widespread grouse species; black grouse, willow grouse and rock ptarmigan. This allowed the tracking of the effective population size (Ne ) of all three species beyond 1 Mya, revealing that (i) early Pleistocene cooling (~2.5Mya) caused an increase in the willow grouse and rock ptarmigan populations, (ii) the mid-Brunhes event (~430kya) and following climatic oscillations decreased the Ne of willow grouse and rock ptarmigan, but increased the Ne of black grouse and (iii) all three species reacted differently to the last glacial maximum (LGM) - black grouse increased prior to it, rock ptarmigan experienced a severe bottleneck and willow grouse was maintained at large population size. We postulate that the varying psmc signal throughout the LGM depicts only the local history of the species. Nevertheless, the large population fluctuations in willow grouse and rock ptarmigan indicate that both species are opportunistic breeders while black grouse tracks the climatic changes more slowly and is maintained at lower Ne . Our results highlight the usefulness of the psmc approach in investigating species' reaction to climate change in the deep past, but also that caution should be taken in drawing general conclusions about the recent past.