scholarly journals Detecting and visualising the impact of heterogeneous evolutionary processes on phylogenetic estimates

2019 ◽  
Author(s):  
Lars S Jermiin ◽  
David R Lovell ◽  
Bernhard Misof ◽  
Peter G Foster ◽  
John Robinson
Keyword(s):  
Sequence Data ◽  
Evolutionary Processes ◽  
Model Based ◽  
Phylogenetic Methods ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
The Impact

AbstractMost model-based molecular phylogenetic methods assume that the sequences diverged on a tree under homogeneous conditions. If evolution occurred under these conditions, then it is unlikely that the sequences would become compositionally heterogeneous. Conversely, if the sequences are compositionally heterogeneous, then it is unlikely that they have evolved under homogeneous conditions. We present methods to detect and analyse heterogeneous evolution in aligned sequence data and to examine—visually and numerically—its effect on phylogenetic estimates. The methods are implemented in three programs, allowing users to better examine under what conditions their phylogenetic data may have evolved.

scholarly journals Measuring Historical and Compositional Signals in Phylogenetic Data

2020 ◽  
Author(s):  
Lars S Jermiin ◽  
Bernhard Misof
Keyword(s):  
Phylogenetic Analysis ◽  
Model Selection ◽  
Simulated Data ◽  
Evolutionary Processes ◽  
Multiple Sequence ◽  
Phylogenetic Methods ◽  
Phylogenetic Data ◽  
Molecular Phylogenetic ◽  
Full Symmetry ◽  
Time Of Divergence

AbstractMost commonly-used molecular phylogenetic methods assume that the sequences evolved on a single bifurcating tree and that the evolutionary processes operating at the variable sites are Markovian. Typically, it is also assumed that these evolutionary processes were stationary, reversible and homogenous across the edges of the tree and that the multiple substitutions at variable sites occurred so infrequently that the historical signal (i.e., the signal in DNA that is due to the order and time of divergence event) in phylogenetic data has been retained, allowing for accurate phylogenetic estimates to be obtained from the data. Here, we present two metrics, λ and δCFS, to quantify the strength of the historical and compositional signals in phylogenetic data. λ quantifies loss of historical signal, with λ = 0.0 indicating evidence of a strong historical signal and λ = 1.0 indicating evidence of a fully eroded historical signal. δCFS quantifies compositional distance from full symmetry of a divergence matrix generated by comparing two sequences, with δCFS = 0.0 indicating no evidence of evolution under dissimilar conditions and δCFS > 0.0 indicating increasing evidence of lineages diverging under different conditions. The metrics are implemented in methods intended for use after multiple sequence alignment and before model selection and phylogenetic analysis. Results generated using these methods allow users of phylogenetic tools to select phylogenetic data more wisely than it previously was possible. The merits of these metrics and methods are illustrated using simulated data and multi-gene alignments obtained from 144 insect genomes.

scholarly journals An Evolutionary Model-Based Approach To Quantify the Genetic Barrier to Drug Resistance in Fast-Evolving Viruses and Its Application to HIV-1 Subtypes and Integrase Inhibitors

2019 ◽  
Vol 63 (8) ◽  
Author(s):  
Kristof Theys ◽  
Pieter J. K. Libin ◽  
Kristel Van Laethem ◽  
Ana B. Abecasis
Keyword(s):  
Sequence Data ◽  
Evolutionary Model ◽  
Integrase Inhibitors ◽  
Genetic Barrier ◽  
Viral Pathogens ◽  
Model Based ◽  
Subtype B ◽  
Genetic Potential ◽  
The Impact ◽  
Hiv 1

ABSTRACT Viral pathogens causing global disease burdens are often characterized by high rates of evolutionary changes. The extensive viral diversity at baseline can shorten the time to escape from therapeutic or immune selective pressure and alter mutational pathways. The impact of genotypic background on the barrier to resistance can be difficult to capture, particularly for agents in experimental stages or that are recently approved or expanded into new patient populations. We developed an evolutionary model-based counting method to quickly quantify the population genetic potential to resistance and assess population differences. We demonstrate its applicability to HIV-1 integrase inhibitors, as their increasing use globally contrasts with limited availability of non-B subtype resistant sequence data and corresponding knowledge gap. A large sequence data set encompassing most prevailing HIV-1 subtypes and resistance-associated mutations of currently approved integrase inhibitors was investigated. A complex interplay between codon predominance, polymorphisms, and associated evolutionary costs resulted in a subtype-dependent varied genetic potential for 15 resistance mutations against integrase inhibitors. While we confirm the lower genetic barrier of subtype B for G140S, we convincingly discard a similar effect previously suggested for G140C. A supplementary analysis for HIV-1 reverse transcriptase inhibitors identified a lower genetic barrier for K65R in subtype C through differential codon usage not reported before. To aid evolutionary interpretations of genomic differences for antiviral strategies, we advanced existing counting methods with increased sensitivity to identify subtype dependencies of resistance emergence. Future applications include novel HIV-1 drug classes or vaccines, as well as other viral pathogens.

scholarly journals Species Diversity of the Pleurostomatid Ciliate Genus Amphileptus (Ciliophora, Haptoria), With Notes on the Taxonomy and Molecular Phylogeny of Three Species

2021 ◽  
Vol 8 ◽  
Author(s):  
Lei Wu ◽  
Jiqiu Li ◽  
Alan Warren ◽  
Xiaofeng Lin
Keyword(s):  
Species Diversity ◽  
Sequence Data ◽  
Southern China ◽  
Phylogenetic Analyses ◽  
Phylogenetic Methods ◽  
Wide Range ◽  
Rdna Sequence Data ◽  
Molecular Phylogenetic ◽  
Intensive Sampling ◽  
High Diversity

Amphileptus is one of the largest genera of pleurostomatid ciliates and its species diversity has been reported in various habitats all over the world. In the present work, we review its biodiversity based on data with reliable morphological records. Our work confirms that there are 50 valid Amphileptus species, some of which have a wide range of salinity adaptability and diverse lifestyles. This genus has a high diversity in China but this might be because of the relatively intensive sampling. Phylogenetic analyses based on SSU rDNA sequence data verify the non-monophyly of the genus Amphileptus. Furthermore, two new and one poorly known Amphileptus species, namely A. shenzhenensis sp. n., A. cocous sp. n., and A. multinucleatusWang, 1934, from coastal habitats of southern China were investigated using morphological and molecular phylogenetic methods. These three species are highly similar based on their contractile vacuoles and macronuclear nodules. However, they can be discriminated by details of their living morphology and somatic kineties. We also propose two new combinations, Amphileptus polymicronuclei (Li, 1990) comb. n. (original combination Hemiophrys polymicronucleiLi, 1990) and Amphileptus salimicus (Burkovsky, 1970b) comb. n. (original combination Hemiophrys salimicaBurkovsky, 1970b).

scholarly journals PSI-40 Two mitochondrial lineages revealed in North American yak

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 477-477
Author(s):  
Leah K Treffer ◽  
Edward S Rice ◽  
Anna M Fuller ◽  
Samuel Cutler ◽  
Jessica L Petersen
Keyword(s):  
Sequence Data ◽  
Haplotype Network ◽  
Ovis Aries ◽  
Similar Species ◽  
Nucleotide Polymorphisms ◽  
Mt Dna ◽  
Protein Coding ◽  
Sister Clade ◽  
Mtdna Sequence ◽  
The Impact

Abstract Domestic yak (Bos grunniens) are bovids native to the Asian Qinghai-Tibetan Plateau. Studies of Asian yak have revealed that introgression with domestic cattle has contributed to the evolution of the species. When imported to North America (NA), some hybridization with B. taurus did occur. The objective of this study was to use mitochondrial (mt) DNA sequence data to better understand the mtDNA origin of NA yak and their relationship to Asian yak and related species. The complete mtDNA sequence of 14 individuals (12 NA yak, 1 Tibetan yak, 1 Tibetan B. indicus) was generated and compared with sequences of similar species from GeneBank (B. indicus, B. grunniens (Chinese), B. taurus, B. gaurus, B. primigenius, B. frontalis, Bison bison, and Ovis aries). Individuals were aligned to the B. grunniens reference genome (ARS_UNL_BGru_maternal_1.0), which was also included in the analyses. The mtDNA genes were annotated using the ARS-UCD1.2 cattle sequence as a reference. Ten unique NA yak haplotypes were identified, which a haplotype network separated into two clusters. Variation among the NA haplotypes included 93 nonsynonymous single nucleotide polymorphisms. A maximum likelihood tree including all taxa was made using IQtree after the data were partitioned into twenty-two subgroups using PartitionFinder2. Notably, six NA yak haplotypes formed a clade with B. indicus; the other four haplotypes grouped with B. grunniens and fell as a sister clade to bison, gaur and gayal. These data demonstrate two mitochondrial origins of NA yak with genetic variation in protein coding genes. Although these data suggest yak introgression with B. indicus, it appears to date prior to importation into NA. In addition to contributing to our understanding of the species history, these results suggest the two major mtDNA haplotypes in NA yak may functionally differ. Characterization of the impact of these differences on cellular function is currently underway.

scholarly journals A Model-Based Tool for Assessing the Impact of Land Use Change Scenarios on Flood Risk in Small-Scale River Systems—Part 1: Pre-Processing of Scenario Based Flood Characteristics for the Current State of Land Use

Hydrology ◽  
2021 ◽  
Vol 8 (3) ◽  
pp. 102
Author(s):  
Frauke Kachholz ◽  
Jens Tränckner
Keyword(s):  
Land Use ◽  
River Flow ◽  
Land Use Changes ◽  
Small Rivers ◽  
Small Scale ◽  
Model Parameters ◽  
Ungauged Catchments ◽  
Model Based ◽  
Current State ◽  
The Impact

Land use changes influence the water balance and often increase surface runoff. The resulting impacts on river flow, water level, and flood should be identified beforehand in the phase of spatial planning. In two consecutive papers, we develop a model-based decision support system for quantifying the hydrological and stream hydraulic impacts of land use changes. Part 1 presents the semi-automatic set-up of physically based hydrological and hydraulic models on the basis of geodata analysis for the current state. Appropriate hydrological model parameters for ungauged catchments are derived by a transfer from a calibrated model. In the regarded lowland river basins, parameters of surface and groundwater inflow turned out to be particularly important. While the calibration delivers very good to good model results for flow (Evol =2.4%, R = 0.84, NSE = 0.84), the model performance is good to satisfactory (Evol = −9.6%, R = 0.88, NSE = 0.59) in a different river system parametrized with the transfer procedure. After transferring the concept to a larger area with various small rivers, the current state is analyzed by running simulations based on statistical rainfall scenarios. Results include watercourse section-specific capacities and excess volumes in case of flooding. The developed approach can relatively quickly generate physically reliable and spatially high-resolution results. Part 2 builds on the data generated in part 1 and presents the subsequent approach to assess hydrologic/hydrodynamic impacts of potential land use changes.

scholarly journals A Reference Framework to Combine Model-Based Design and AR to Improve Social Sustainability

2021 ◽  
Vol 13 (4) ◽  
pp. 2031
Author(s):  
Fabio Grandi ◽  
Riccardo Karim Khamaisi ◽  
Margherita Peruzzini ◽  
Roberto Raffaeli ◽  
Marcello Pellicciari
Keyword(s):  
Positive Impact ◽  
Cost Effective ◽  
Digital Models ◽  
Model Based ◽  
Digital Contents ◽  
Recent Developments ◽  
Virtual Simulations ◽  
Product And Process ◽  
The Impact ◽  
Time Information

Product and process digitalization is pervading numerous areas in the industry to improve quality and reduce costs. In particular, digital models enable virtual simulations to predict product and process performances, as well as to generate digital contents to improve the general workflow. Digital models can also contain additional contents (e.g., model-based design (MBD)) to provide online and on-time information about process operations and management, as well as to support operator activities. The recent developments in augmented reality (AR) offer new specific interfaces to promote the great diffusion of digital contents into industrial processes, thanks to flexible and robust applications, as well as cost-effective devices. However, the impact of AR applications on sustainability is still poorly explored in research. In this direction, this paper proposed an innovative approach to exploit MBD and introduce AR interfaces in the industry to support human intensive processes. Indeed, in those processes, the human contribution is still crucial to guaranteeing the expected product quality (e.g., quality inspection). The paper also analyzed how this new concept can benefit sustainability and define a set of metrics to assess the positive impact on sustainability, focusing on social aspects.

scholarly journals Model-Based Control of Torque and Nitrogen Oxide Emissions in a Euro VI 3.0 L Diesel Engine through Rapid Prototyping

Energies ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1107
Author(s):  
Stefano d’Ambrosio ◽  
Roberto Finesso ◽  
Gilles Hardy ◽  
Andrea Manelli ◽  
Alessandro Mancarella ◽  
...  
Keyword(s):  
Diesel Engine ◽  
Rapid Prototyping ◽  
Nitrogen Oxide ◽  
Thermal State ◽  
Pollutant Emissions ◽  
Computational Time ◽  
Nox Emissions ◽  
Model Based ◽  
Brake Mean Effective Pressure ◽  
The Impact

In the present paper, a model-based controller of engine torque and engine-out Nitrogen oxide (NOx) emissions, which was previously developed and tested by means of offline simulations, has been validated on a FPT F1C 3.0 L diesel engine by means of rapid prototyping. With reference to the previous version, a new NOx model has been implemented to improve robustness in terms of NOx prediction. The experimental tests have confirmed the basic functionality of the controller in transient conditions, over different load ramps at fixed engine speeds, over which the average RMSE (Root Mean Square Error) values for the control of NOx emissions were of the order of 55–90 ppm, while the average RMSE values for the control of brake mean effective pressure (BMEP) were of the order of 0.25–0.39 bar. However, the test results also highlighted the need for further improvements, especially concerning the effect of the engine thermal state on the NOx emissions in transient operation. Moreover, several aspects, such as the check of the computational time, the impact of the controller on other pollutant emissions, or on the long-term engine operations, will have to be evaluated in future studies in view of the controller implementation on the engine control unit.

A decision making model based on fuzzy inference to predict the impact of SCOR® indicators on customer perceived value

2020 ◽  
Vol 223 ◽  
pp. 107520
Author(s):  
Lucas Gabriel Zanon ◽  
Rafael Ferro Munhoz Arantes ◽  
Lucas Daniel Del Rosso Calache ◽  
Luiz Cesar Ribeiro Carpinetti
Keyword(s):  
Decision Making ◽  
Fuzzy Inference ◽  
Perceived Value ◽  
Model Based ◽  
Customer Perceived Value ◽  
Decision Making Model ◽  
The Impact

The impact of global change on the hydropower potential of Europe: a model-based analysis

Energy Policy ◽  
2005 ◽  
Vol 33 (7) ◽  
pp. 839-855 ◽  
Author(s):  
Bernhard Lehner ◽  
Gregor Czisch ◽  
Sara Vassolo
Keyword(s):  
Global Change ◽  
Model Based ◽  
Hydropower Potential ◽  
The Impact ◽  
Model Based Analysis

Research and Improvement of the Keep-Right-Except-to-Pass Rule

2014 ◽  
Vol 915-916 ◽  
pp. 459-463
Author(s):  
He Quan Zhang
Keyword(s):  
Fluid Mechanics ◽  
Traffic Flow ◽  
Influence Factors ◽  
Traffic Model ◽  
Light Traffic ◽  
The Road ◽  
Model Based ◽  
Light Passing ◽  
Improved Model ◽  
The Impact

In order to deal with the impact on traffic flow of the rule, we compare the influence factors of traffic flow (passing, etc.) into viscous resistance of fluid mechanics, and establish a traffic model based on fluid mechanics. First, in heavy and light traffic, we respectively use this model to simulate the actual segment of the road and find that when the traffic is heavy, the rule hinder the further increase in traffic. For this reason, we make further improvements to the model to obtain a fluid traffic model based on no passing and find that the improved model makes traffic flow increase significantly. Then, the improved model is applied to the light traffic, we find there are no significant changes in traffic flow .In this regard we propose a new rule: when the traffic is light, passing is allowed, but when the traffic is heavy, passing is not allowed.

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