scholarly journals Positive selection on mitochondria may eliminate heritable microbes from arthropod populations

2021 ◽  
Vol 288 (1959) ◽  
Author(s):  
Andy Fenton ◽  
M. Florencia Camus ◽  
Gregory D. D. Hurst
Keyword(s):  
Positive Selection ◽  
Population Genetic ◽  
Infected Individual ◽  
Mean Field ◽  
Low Frequency ◽  
Direct Selection ◽  
Correlated Response ◽  
Mtdna Mutation ◽  
The Impact ◽  
Mtdna Marker

Diverse eukaryotic taxa carry facultative heritable symbionts, microbes that are passed from mother to offspring. These symbionts are coinherited with mitochondria, and selection favouring either new symbionts, or new symbiont variants, is known to drive loss of mitochondrial diversity as a correlated response. More recently, evidence has accumulated of episodic directional selection on mitochondria, but with currently unknown consequences for symbiont evolution. We therefore employed a population genetic mean field framework to model the impact of selection on mitochondrial DNA (mtDNA) upon symbiont frequency for three generic scenarios of host–symbiont interaction. Our models predict that direct selection on mtDNA can drive symbionts out of the population where a positively selected mtDNA mutation occurs initially in an individual that is uninfected with the symbiont, and the symbiont is initially at low frequency. When, by contrast, the positively selected mtDNA mutation occurs in a symbiont-infected individual, the mutation becomes fixed and in doing so removes symbiont variation from the population. We conclude that the molecular evolution of symbionts and mitochondria, which has previously been viewed from a perspective of selection on symbionts driving the evolution of a neutral mtDNA marker, should be reappraised in the light of positive selection on mtDNA.

scholarly journals Positive selection on mitochondria may eliminate heritable microbes from arthropod populations.

2021 ◽  
Author(s):  
Andy Fenton ◽  
Florencia Camus ◽  
Gregory D D Hurst
Keyword(s):  
Positive Selection ◽  
Infected Individual ◽  
Natural Populations ◽  
Low Frequency ◽  
Direct Selection ◽  
Correlated Response ◽  
Mtdna Mutation ◽  
Maternal Line ◽  
Arthropod Species ◽  
The Impact

The majority of arthropod species carry facultative heritable microbes, bacteria that are passed from mother to offspring, and which may contribute to host function. These symbionts are coinherited down the maternal line with mitochondria, and selection favouring either new symbionts, or new symbiont variants, is known to drive loss of mitochondrial diversity as a correlated response. More recently, evidence has accumulated of episodic directional selection on mitochondria. We therefore examined the reciprocal interaction and model the impact of selection on mitochondrial DNA (mtDNA) on symbiont frequency. We performed this for three generic scenarios: a fixed benefit to the host carrying the symbiont, a benefit that decreased with symbiont frequency, and a benefit that increased with symbiont frequency. We find that direct selection on mtDNA can drive symbionts out of the population under some circumstances. Symbiont extinction occurs where the positively selected mtDNA mutation occurs initially in an individual that is uninfected with the symbiont, and the symbiont is initially at low frequency. When, in contrast, the positively selected mtDNA mutation occurs in a symbiont infected individual, the mutation becomes fixed and in doing so removes symbiont variation from the population. Given low frequency symbiont infections are common in natural populations, and selection on mtDNA is also considered to occur frequently, we conclude that mtDNA driven loss of symbionts represents a novel mechanism driving loss of facultative heritable microbes. We conclude further that the molecular evolution of symbionts and mitochondria, which has previously been viewed from a perspective of selection on symbionts driving the evolution of a neutral mtDNA marker, should be reappraised in the light of positive selection on mtDNA. Where low mtDNA and symbiont genetic diversity are observed, it should not be assumed to be a consequences of selection acting on the symbiont.

scholarly journals How Local Interactions Impact the Dynamics of an Epidemic

2021 ◽  
Vol 83 (12) ◽  
Author(s):  
Lydia Wren ◽  
Alex Best
Keyword(s):  
Disease Transmission ◽  
Infected Individual ◽  
Mean Field ◽  
Stochastic Simulations ◽  
Disease Spread ◽  
Pair Approximation ◽  
Human Populations ◽  
Local Interactions ◽  
Equal Chance ◽  
The Impact

AbstractSusceptible–Infected–Recovered (SIR) models have long formed the basis for exploring epidemiological dynamics in a range of contexts, including infectious disease spread in human populations. Classic SIR models take a mean-field assumption, such that a susceptible individual has an equal chance of catching the disease from any infected individual in the population. In reality, spatial and social structure will drive most instances of disease transmission. Here we explore the impacts of including spatial structure in a simple SIR model. We combine an approximate mathematical model (using a pair approximation) and stochastic simulations to consider the impact of increasingly local interactions on the epidemic. Our key development is to allow not just extremes of ‘local’ (neighbour-to-neighbour) or ‘global’ (random) transmission, but all points in between. We find that even medium degrees of local interactions produce epidemics highly similar to those with entirely global interactions, and only once interactions are predominantly local do epidemics become substantially lower and later. We also show how intervention strategies to impose local interactions on a population must be introduced early if significant impacts are to be seen.

USING FIELD DATA FOR THE EVALUATION OF THE IMPACT OF ULTRA-LOW FREQUENCY MOTIONS ON THE FATIGUE OF MOORING LINES

2019 ◽  
Author(s):  
Guilherme Borzacchiello ◽  
Carl Albrecht ◽  
Fabricio N Correa ◽  
Breno Jacob ◽  
Guilherme da Silva Leal
Keyword(s):  
Field Data ◽  
Low Frequency ◽  
Mooring Lines ◽  
The Impact

Systematic benchmark of ancient DNA read mapping

2021 ◽  
Author(s):  
Adrien Oliva ◽  
Raymond Tobler ◽  
Alan Cooper ◽  
Bastien Llamas ◽  
Yassine Souilmi
Keyword(s):  
Ancient Dna ◽  
Dna Sequences ◽  
Population Genetic ◽  
Reference Genome ◽  
Population Data ◽  
Human Populations ◽  
Current Standard ◽  
Read Mapping ◽  
Reference Bias ◽  
The Impact

Abstract The current standard practice for assembling individual genomes involves mapping millions of short DNA sequences (also known as DNA ‘reads’) against a pre-constructed reference genome. Mapping vast amounts of short reads in a timely manner is a computationally challenging task that inevitably produces artefacts, including biases against alleles not found in the reference genome. This reference bias and other mapping artefacts are expected to be exacerbated in ancient DNA (aDNA) studies, which rely on the analysis of low quantities of damaged and very short DNA fragments (~30–80 bp). Nevertheless, the current gold-standard mapping strategies for aDNA studies have effectively remained unchanged for nearly a decade, during which time new software has emerged. In this study, we used simulated aDNA reads from three different human populations to benchmark the performance of 30 distinct mapping strategies implemented across four different read mapping software—BWA-aln, BWA-mem, NovoAlign and Bowtie2—and quantified the impact of reference bias in downstream population genetic analyses. We show that specific NovoAlign, BWA-aln and BWA-mem parameterizations achieve high mapping precision with low levels of reference bias, particularly after filtering out reads with low mapping qualities. However, unbiased NovoAlign results required the use of an IUPAC reference genome. While relevant only to aDNA projects where reference population data are available, the benefit of using an IUPAC reference demonstrates the value of incorporating population genetic information into the aDNA mapping process, echoing recent results based on graph genome representations.

scholarly journals Evaluation of P-Band SAR Tomography for Mapping Tropical Forest Vertical Backscatter and Tree Height

2021 ◽  
Vol 13 (8) ◽  
pp. 1485
Author(s):  
Naveen Ramachandran ◽  
Sassan Saatchi ◽  
Stefano Tebaldini ◽  
Mauro Mariotti d’Alessandro ◽  
Onkar Dikshit
Keyword(s):  
Tropical Forest ◽  
Vertical Profile ◽  
Mean Squared Error ◽  
Low Frequency ◽  
Tree Height ◽  
Canopy Layer ◽  
Local Maxima ◽  
Slope Correction ◽  
Compensation Approach ◽  
The Impact

Low-frequency tomographic synthetic aperture radar (TomoSAR) techniques provide an opportunity for quantifying the dynamics of dense tropical forest vertical structures. Here, we compare the performance of different TomoSAR processing, Back-projection (BP), Capon beamforming (CB), and MUltiple SIgnal Classification (MUSIC), and compensation techniques for estimating forest height (FH) and forest vertical profile from the backscattered echoes. The study also examines how polarimetric measurements in linear, compact, hybrid, and dual circular modes influence parameter estimation. The tomographic analysis was carried out using P-band data acquired over the Paracou study site in French Guiana, and the quantitative evaluation was performed using LiDAR-based canopy height measurements taken during the 2009 TropiSAR campaign. Our results show that the relative root mean squared error (RMSE) of height was less than 10%, with negligible systematic errors across the range, with Capon and MUSIC performing better for height estimates. Radiometric compensation, such as slope correction, does not improve tree height estimation. Further, we compare and analyze the impact of the compensation approach on forest vertical profiles and tomographic metrics and the integrated backscattered power. It is observed that radiometric compensation increases the backscatter values of the vertical profile with a slight shift in local maxima of the canopy layer for both the Capon and the MUSIC estimators. Our results suggest that applying the proper processing and compensation techniques on P-band TomoSAR observations from space will allow the monitoring of forest vertical structure and biomass dynamics.

scholarly journals Shift Detection in Hydrological Regimes and Pluriannual Low-Frequency Streamflow Forecasting Using the Hidden Markov Model

Water ◽  
2020 ◽  
Vol 12 (7) ◽  
pp. 2058 ◽  
Author(s):  
Larissa Rolim ◽  
Francisco de Souza Filho
Keyword(s):  
Time Series ◽  
Markov Model ◽  
Hidden Markov Model ◽  
Extreme Events ◽  
Hidden Markov ◽  
Low Frequency ◽  
Streamflow Forecasting ◽  
Hydrologic Time Series ◽  
Low Frequency Variability ◽  
The Impact

Improved water resource management relies on accurate analyses of the past dynamics of hydrological variables. The presence of low-frequency structures in hydrologic time series is an important feature. It can modify the probability of extreme events occurring in different time scales, which makes the risk associated with extreme events dynamic, changing from one decade to another. This article proposes a methodology capable of dynamically detecting and predicting low-frequency streamflow (16–32 years), which presented significance in the wavelet power spectrum. The Standardized Runoff Index (SRI), the Pruned Exact Linear Time (PELT) algorithm, the breaks for additive seasonal and trend (BFAST) method, and the hidden Markov model (HMM) were used to identify the shifts in low frequency. The HMM was also used to forecast the low frequency. As part of the results, the regime shifts detected by the BFAST approach are not entirely consistent with results from the other methods. A common shift occurs in the mid-1980s and can be attributed to the construction of the reservoir. Climate variability modulates the streamflow low-frequency variability, and anthropogenic activities and climate change can modify this modulation. The identification of shifts reveals the impact of low frequency in the streamflow time series, showing that the low-frequency variability conditions the flows of a given year.

scholarly journals Corrigendum to: Consequences of genetic selection for environmental impact traits on economically important traits in dairy cows

2018 ◽  
Vol 58 (10) ◽  
pp. 1966
Author(s):  
Purna Kandel ◽  
Sylvie Vanderick ◽  
Marie-Laure Vanrobays ◽  
Hélène Soyeurt ◽  
Nicolas Gengler
Keyword(s):  
Dairy Cows ◽  
Body Condition Score ◽  
Genetic Correlations ◽  
Genetic Selection ◽  
Selection Response ◽  
Direct Selection ◽  
Correlated Response ◽  
Production Traits ◽  
Ch4 Emissions ◽  
Natural Logarithm

Methane (CH4) emission is an important environmental trait in dairy cows. Breeding aiming to mitigate CH4 emissions require the estimation of genetic correlations with other economically important traits and the prediction of their selection response. In this study, test-day CH4 emissions were predicted from milk mid-infrared spectra of Holstein cows. Predicted CH4 emissions (PME) and log-transformed CH4 intensity (LMI) computed as the natural logarithm of PME divided by milk yield (MY). Genetic correlations of PME and LMI with traits used currently were approximated from correlations between estimated breeding values of sires. Values were for PME with MY 0.06, fat yield (FY) 0.09, protein yield (PY) 0.13, fertility 0.17; body condition score (BCS) –0.02; udder health (UDH) 0.22; and longevity 0.22. As expected by its definition, values were negative for LMI with production traits (MY –0.61; FY –0.15 and PY –0.40) and positive with fertility (0.36); BCS (0.20); UDH (0.08) and longevity (0.06). The genetic correlations of 33 type traits with PME ranged from –0.12 to 0.25 and for LMI ranged from –0.22 to 0.18. Without selecting PME and LMI (status quo) the relative genetic change through correlated responses of other traits were in PME by 2% and in LMI by –15%, but only due to the correlated response to MY. Results showed for PME that direct selection of this environmental trait would reduce milk carbon foot print but would also affect negatively fertility. Therefore, more profound changes in current indexes will be required than simply adding environmental traits as these traits also affect the expected progress of other traits.

scholarly journals Polytetrafluoroethylene Films in Rigid Polyurethane Foams’ Dielectric Permittivity Measurements with a One-Side Access Capacitive Sensor

Polymers ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1173
Author(s):  
Ilze Beverte ◽  
Ugis Cabulis ◽  
Sergejs Gaidukovs
Keyword(s):  
Dielectric Properties ◽  
Dielectric Permittivity ◽  
Low Frequency ◽  
Capacitive Sensor ◽  
Polyurethane Foams ◽  
Active Area ◽  
Ptfe Film ◽  
Practical Applications ◽  
Permittivity Measurements ◽  
The Impact

As a non-metallic composite material, widely applied in industry, rigid polyurethane (PUR) foams require knowledge of their dielectric properties. In experimental determination of PUR foams’ dielectric properties protection of one-side capacitive sensor’s active area from adverse effects caused by the PUR foams’ test objects has to be ensured. In the given study, the impact of polytetrafluoroethylene (PTFE) films, thickness 0.20 mm and 0.04 mm, in covering or simulated coating the active area of one-side access capacitive sensor’ electrodes on the experimentally determined true dielectric permittivity spectra of rigid PUR foams is estimated. Penetration depth of the low frequency excitation field into PTFE and PUR foams is determined experimentally. Experiments are made in order to evaluate the difference between measurements on single PUR foams’ samples and on complex samples “PUR foams + PTFE film” with two calibration modes. A modification factor and a small modification criterion are defined and values of modifications are estimated in numerical calculations. Conclusions about possible practical applications of PTFE films in dielectric permittivity measurements of rigid PUR foams with one-side access capacitive sensor are made.

Abstract P315: Increase in Stress May Contribute to Lower Heart Rate Variability in Healthy Young Subjects

Circulation ◽  
2012 ◽  
Vol 125 (suppl_10) ◽  
Author(s):  
Amanda C Costa ◽  
Ana Gabriela C Silva ◽  
Cibele T Ribeiro ◽  
Guilherme A Fregonezi ◽  
Fernando A Dias
Keyword(s):  
Cardiovascular Disease ◽  
Heart Rate ◽  
Heart Rate Variability ◽  
Healthy Volunteers ◽  
Perceived Stress ◽  
Low Frequency ◽  
Statistical Correlation ◽  
Total Power ◽  
The Impact ◽  
Nonparametric Correlation

Background: Stress is one of the risk factors for cardiovascular disease and decreased heart rate variability is associated to increased mortality in some cardiac diseases. The aim of the study was to assess the impact of perceived stress on cardiac autonomic regulation in young healthy volunteers. Methods: 35 young healthy volunteers (19 to 29 years old, 6 men) from a Brazilian population were assessed for perceived stress by the translated and validated Perceived Stress Scale (PSS, 14 questions) and had the R-R intervals recorded at rest on supine position (POLAR RS800CX) and analyzed (5 minutes, Kubius HRV software) by Fast-Fourier Transform for quantification of Heart Rate Variability (HRV). Results: Average data (±SD) for age, heart rate, BMI, waist circumference and percentage of body fat (%BF) were: 21.3±2.7 years; 65.5±7.9 bpm; 22.3±1.9 Kg/m 2 ; 76.0±6.1 cm and 32.1±6.6%; respectively. The mean score for the PSS-14 was 23.5±7.2 and for the HRV parameter as follow: SSDN=54.8±21.2ms; rMSSD=55.9±32.2ms; low-frequency (LF)= 794.8±579.7ms 2 ; High-frequency (HF)= 1508.0±1783.0 ms 2 ; LF(n.u.)= 41.1±16.2; HF(n.u.)= 58.9±16.2; LF/HF=0.89±0.80 and Total power (TP)= 3151±2570ms 2 . Spearman nonparametric correlation was calculated and there was a significant correlation of PSS-14 scores and LF (ms 2 ) (r=−0.343; p= 0.044). Other HRV variables did not shown significant correlation but also had negative values for Spearman r (TP r=−0.265, p=0.124; HF r=−0.158; SSDN r=−0.207; rMSSD r=−0.243, p=0.160). LF/HF and LF(n.u.) did not correlate to PSS-14 having Spearman r very close to zero (LF/HF r=−0.007, p=0.969; LF(n.u.) r=−0.005, p=0.976). No correlation was found for HRV parameters and BMI and there was a trend for statistical correlation of %BF and LF (ms 2 ) (r=−0.309, p=0.071). Conclusions: These data demonstrate a possible association of perceived stress level and HRV at rest. Changes in LF can be a consequence of both sympathetic and parasympathetic activity, however, analyzing the other variables HF, TP, SSDN and rMSSD (all negative Spearman r) and due to the lack of changes in LF/HF ratio and LF(n.u.) we interpret that increased stress may be associated to decrease in overall heart rate variability. These changes were seen in healthy individuals and may point out an important mechanism in cardiovascular disease development.

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