scholarly journals Quantifying eco-evolutionary contributions to trait divergence in spatially structured systems

2019 ◽  
Author(s):  
Lynn Govaert ◽  
Jelena H. Pantel ◽  
Luc De Meester
Keyword(s):  
Genetic Differentiation ◽  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Temporal Dynamics ◽  
Similar Time ◽  
Spatial Studies ◽  
Trait Divergence ◽  
Structured Systems ◽  
Evolutionary Genetic ◽  
Over Time

AbstractEcological and evolutionary processes can occur at similar time scales, and hence influence one another. There has been much progress in the development of metrics that quantify contributions of ecological and evolutionary components to trait change over time. However, many empirical evolutionary ecology studies document genetic differentiation among populations structured in space. In both time and space, the observed differentiation in trait values among populations and communities can be the result of interactions between non-evolutionary (phenotypic plasticity, changes in the relative abundance of species) and evolutionary (genetic differentiation among populations) processes. However, the tools developed so far to quantify ecological and evolutionary contributions to trait change are implicitly addressing temporal dynamics because they require directionality of change from an ancestral to a derived state. Identifying directionality from one site to another in spatial studies of eco-evolutionary dynamics is not always possible and often not desired. We here suggest three modifications to existing metrics so they allow the partitioning of ecological and evolutionary contributions to changes in population and community trait values across landscapes. Applying these spatially modified metrics to published empirical examples shows how these metrics can be used to generate new empirical insights and to facilitate future comparative analyses. The possibility to apply eco-evolutionary partitioning metrics to populations and communities in real landscapes is critical as it will broaden our capacity to quantify eco-evolutionary interactions as they occur in nature.

scholarly journals EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Chandler D. Gatenbee ◽  
Ryan O. Schenck ◽  
Rafael R. Bravo ◽  
Alexander R. A. Anderson
Keyword(s):  
High Throughput ◽  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Sequence Data ◽  
Single Point ◽  
Model Data ◽  
Genotype Frequencies ◽  
Tool Set ◽  
Over Time

Abstract Background High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population under study by tracking the changes in genotype frequencies over time. This necessitates a simple and flexible means of visualizing an increasingly complex set of data. Results Here we offer EvoFreq as a comprehensive tool set to visualize the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods. EvoFreq expands substantially on previous means of visualizing the clonal, temporal dynamics and offers users a range of options for displaying their sequence or model data. Conclusions EvoFreq, implemented in R with robust user options and few dependencies, offers a high-throughput means of quickly building, and interrogating the temporal dynamics of hereditary information across many systems. EvoFreq is freely available via https://github.com/MathOnco/EvoFreq.

scholarly journals EvoFreq: Visualization of the Evolutionary Frequencies of Sequence and Model Data

2019 ◽  
Author(s):  
Chandler D. Gatenbee ◽  
Ryan O. Schenck ◽  
Rafael Bravo ◽  
Alexander R.A. Anderson
Keyword(s):  
High Throughput ◽  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Sequence Data ◽  
Single Point ◽  
Model Data ◽  
Genotype Frequencies ◽  
Tool Set ◽  
Over Time

AbstractHigh throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population under study by tracking the changes in genotype frequencies over time. This necessitates a simple and flexible means of visualizing an increasingly complex set of data. Here we offer EvoFreq as a comprehensive tool set to visualize the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods. EvoFreq expands substantially on previous means of visualizing the clonal, temporal dynamics and offers users a range of options for displaying their sequence or model data. EvoFreq, implemented in R with robust user options and few dependencies, offers a high-throughput means of quickly building, and interrogating the temporal dynamics of hereditary information across many systems. EvoFreq is freely available via https://github.com/MathOnco/EvoFreq.

scholarly journals Evolutionary Ecology of Natural Comammox Nitrospira Populations

mSystems ◽  
2022 ◽  
Author(s):  
Alejandro Palomo ◽  
Arnaud Dechesne ◽  
Otto X. Cordero ◽  
Barth F. Smets
Keyword(s):  
Evolutionary Dynamics ◽  
Evolutionary Ecology ◽  
Single Species ◽  
Evolutionary Processes ◽  
Ecological Processes ◽  
Interacting Species ◽  
Microbial Species ◽  
Experimental Systems ◽  
Over Time

Microbial species interact with each other and their environment (ecological processes) and undergo changes in their genomic repertoire over time (evolutionary processes). How these two classes of processes interact is largely unknown, especially for complex communities, as most studies of microbial evolutionary dynamics consider single species in isolation or a few interacting species in simplified experimental systems.

scholarly journals Acute symptoms of mild to moderate COVID-19 are highly heterogeneous across individuals and over time

2021 ◽  
Author(s):  
Thomas L Rodebaugh ◽  
Madelyn R Frumkin ◽  
Angela M Reiersen ◽  
Eric J Lenze ◽  
Michael S Avidan ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Survey Methods ◽  
Clinical Care ◽  
Clinical Deterioration ◽  
Symptom Profiles ◽  
Fluctuating Course ◽  
The Common ◽  
Symptom Changes ◽  
Over Time

Abstract Background The symptoms of COVID-19 appear to be heterogenous, and the typical course of these symptoms is unknown. Our objectives were to characterize the common trajectories of COVID-19 symptoms and assess how symptom course predicts other symptom changes as well as clinical deterioration. Methods 162 participants with acute COVID-19 responded to surveys up to 31 times for up to 17 days. Several statistical methods were used to characterize the temporal dynamics of these symptoms. Because nine participants showed clinical deterioration, we explored whether these participants showed any differences in symptom profiles. Results Trajectories varied greatly between individuals, with many having persistently severe symptoms or developing new symptoms several days after being diagnosed. A typical trajectory was for a symptom to improve at a decremental rate, with most symptoms still persisting to some degree at the end of the reporting period. The pattern of symptoms over time suggested a fluctuating course for many patients. Participants who showed clinical deterioration were more likely to present with higher reports of severity of cough and diarrhea. Conclusion The course of symptoms during the initial weeks of COVID-19 is highly heterogeneous and is neither predictable nor easily characterized using typical survey methods. This has implications for clinical care and early-treatment clinical trials. Additional research is needed to determine whether the decelerating improvement pattern seen in our data is related to the phenomenon of patients reporting long-term symptoms, and whether higher symptoms of diarrhea in early illness presages deterioration.

scholarly journals Longitudinal Patterns of Ethical Organisational Culture as a Context for Leaders’ Well-Being: Cumulative Effects Over 6 Years

2021 ◽  
Author(s):  
Mari Huhtala ◽  
Muel Kaptein ◽  
Joona Muotka ◽  
Taru Feldt
Keyword(s):  
Latent Profile Analysis ◽  
Temporal Dynamics ◽  
Ethical Dilemmas ◽  
Extended Period ◽  
Well Being ◽  
Organisational Culture ◽  
Cumulative Effects ◽  
Ethical Culture ◽  
Continuous Increase ◽  
Over Time

AbstractThe aim of this longitudinal study was to investigate the temporal dynamics of ethical organisational culture and how it associates with well-being at work when potential changes in ethical culture are measured over an extended period of 6 years. We used a person-centred study design, which allowed us to detect both typical and atypical patterns of ethical culture stability as well as change among a sample of leaders. Based on latent profile analysis and hierarchical linear modelling we found longitudinal, concurrent relations and cumulative gain and loss cycles between different ethical culture patterns and leaders’ well-being. Leaders in the strongest ethical culture pattern experienced the highest level of work engagement and a decreasing level of ethical dilemmas and stress. Leaders who gave the lowest ratings on ethical culture which also decreased over time reported the highest level of ethical dilemmas, stress, and burnout. They also showed a continuous increase in these negative outcomes over time. Thus, ethical culture has significant cumulative effects on well-being, and these longitudinal effects can be both negative and positive, depending on the experienced strength of the culture’s ethicality.

scholarly journals 520. Longitudinal Analysis of SARS-CoV-2 Viruses in Hospitalized Adults

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S325-S326
Author(s):  
Lacy Simons ◽  
Ramon Lorenzo-Redondo ◽  
Hannah Nam ◽  
Scott C Roberts ◽  
Michael G Ison ◽  
...  
Keyword(s):  
Viral Load ◽  
Genome Sequencing ◽  
Viral Genome ◽  
Temporal Dynamics ◽  
Population Level ◽  
Hospital Staff ◽  
Therapeutic Interventions ◽  
Viral Loads ◽  
Qrt Pcr ◽  
Over Time

Abstract Background The rapid spread of SARS-CoV-2, the causative agent of Coronavirus disease 2019 (COVID-19), has been accompanied by the emergence of viral mutations, some of which may have distinct virological and clinical consequences. While whole genome sequencing efforts have worked to map this viral diversity at the population level, little is known about how SARS-CoV-2 may diversify within a host over time. This is particularly important for understanding the emergence of viral resistance to therapeutic interventions and immune pressure. The goal of this study was to assess the change in viral load and viral genome sequence within patients over time and determine if these changes correlate with clinical and/or demographic parameters. Methods Hospitalized patients admitted to Northwestern Memorial Hospital with a positive SARS-CoV-2 test were enrolled in a longitudinal study for the serial collection of nasopharyngeal specimens. Swabs were administered to patients by hospital staff every 4 ± 1 days for up to 32 days or until the patients were discharged. RNA was extracted from each specimen and viral loads were calculated by quantitative reverse transcriptase PCR (qRT-PCR). Specimens with qRT-PCR cycle threshold values less than or equal to 30 were subject to whole viral genome sequencing by reverse transcription, multiplex PCR, and deep sequencing. Variant populations sizes were estimated and subject to phylogenetic analysis relative to publicly available SARS-CoV-2 sequences. Sequence and viral load data were subsequently correlated to available demographic and clinical data. Results 60 patients were enrolled from March 26th to June 20th, 2020. We observed an overall decrease in nasopharyngeal viral load over time across all patients. However, the temporal dynamics of viral load differed on a patient-by-patient basis. Several mutations were also observed to have emerged within patients over time. Distribution of SARS-CoV-2 viral loads in serially collected nasopharyngeal swabs in hospitalized adults as determined by qRT-PCR. Samples were collected every 4 ± 1 days (T#1–8) and viral load is displayed by log(copy number). Conclusion These data indicate that SARS-CoV-2 viral loads in the nasopharynx decrease over time and that the virus can accumulate mutations during replication within individual patients. Future studies will examine if some of these mutations may provide fitness advantages in the presence of therapeutic and/or immune selective pressures. Disclosures Michael G. Ison, MD MS, AlloVir (Consultant)

scholarly journals Fast evolutionary genetic differentiation during experimental colonizations

2013 ◽  
Vol 92 (2) ◽  
pp. 183-194 ◽  
Author(s):  
JOSIANE SANTOS ◽  
MARTA PASCUAL ◽  
PEDRO SIMÕES ◽  
INÊS FRAGATA ◽  
MICHAEL R. ROSE ◽  
...  
Keyword(s):  
Genetic Differentiation ◽  
Evolutionary Genetic

scholarly journals Seed Banks Alter the Rate and Direction of Molecular Evolution in Bacillus subtilis

2021 ◽  
Author(s):  
William R. Shoemaker ◽  
Evgeniya Polezhaeva ◽  
Kenzie B. Givens ◽  
Jay T. Lennon
Keyword(s):  
Bacillus Subtilis ◽  
Molecular Evolution ◽  
Seed Bank ◽  
Negative Selection ◽  
Evolutionary Dynamics ◽  
Genetic Manipulation ◽  
Seed Banks ◽  
Rate Of Molecular Evolution ◽  
Over Time ◽  
Growth And Reproduction

Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which in turn effects the evolution of their respective populations. Many organisms are able to respond to fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e., a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. We find that the ability to enter a dormant state increases the accumulation of genetic diversity over time and alters the trajectory of mutations, findings that are recapitulated using simulations based on a simple mathematical model. While the ability to form a seed bank does not alter the degree of negative selection, we find that it consistently alters the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank affects the direction and rate of molecular evolution over an extended evolutionary timescale.

scholarly journals Temporal Dynamics of Cloacal Microbiota in Adult Laying Chickens With and Without Access to an Outdoor Range

2021 ◽  
Vol 11 ◽  
Author(s):  
Janneke Schreuder ◽  
Francisca C. Velkers ◽  
Alex Bossers ◽  
Ruth J. Bouwstra ◽  
Willem F. de Boer ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Composition ◽  
Intestinal Microbiota ◽  
Environmental Changes ◽  
Temporal Dynamics ◽  
Microbial Community Composition ◽  
Sudden Change ◽  
Rrna Gene ◽  
Poultry House ◽  
Over Time

Associations between animal health and performance, and the host’s microbiota have been recently established. In poultry, changes in the intestinal microbiota have been linked to housing conditions and host development, but how the intestinal microbiota respond to environmental changes under farm conditions is less well understood. To gain insight into the microbial responses following a change in the host’s immediate environment, we monitored four indoor flocks of adult laying chickens three times over 16 weeks, during which two flocks were given access to an outdoor range, and two were kept indoors. To assess changes in the chickens’ microbiota over time, we collected cloacal swabs of 10 hens per flock and performed 16S rRNA gene amplicon sequencing. The poultry house (i.e., the stable in which flocks were housed) and sampling time explained 9.2 and 4.4% of the variation in the microbial community composition of the flocks, respectively. Remarkably, access to an outdoor range had no detectable effect on microbial community composition, the variability of microbiota among chickens of the same flock, or microbiota richness, but the microbiota of outdoor flocks became more even over time. Fluctuations in the composition of the microbiota over time within each poultry house were mainly driven by turnover in rare, rather than dominant, taxa and were unique for each flock. We identified 16 amplicon sequence variants that were differentially abundant over time between indoor and outdoor housed chickens, however none were consistently higher or lower across all chickens of one housing type over time. Our study shows that cloacal microbiota community composition in adult layers is stable following a sudden change in environment, and that temporal fluctuations are unique to each flock. By exploring microbiota of adult poultry flocks within commercial settings, our study sheds light on how the chickens’ immediate environment affects the microbiota composition.

scholarly journals Daptomycin treatment impacts resistance in off-target populations of vancomycin-resistant Enterococcus faecium

PLoS Biology ◽  
2020 ◽  
Vol 18 (12) ◽  
pp. e3000987
Author(s):  
Clare L. Kinnear ◽  
Elsa Hansen ◽  
Valerie J. Morley ◽  
Kevin C. Tracy ◽  
Meghan Forstchen ◽  
...  
Keyword(s):  
Enterococcus Faecium ◽  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Phenotypic Diversity ◽  
Target Selection ◽  
Quantitative Measure ◽  
Target Population ◽  
Control Group ◽  
Antibiotic Exposure ◽  
Hospital System

The antimicrobial resistance crisis has persisted despite broad attempts at intervention. It has been proposed that an important driver of resistance is selection imposed on bacterial populations that are not the intended target of antimicrobial therapy. But to date, there has been limited quantitative measure of the mean and variance of resistance following antibiotic exposure. Here we focus on the important nosocomial pathogen Enterococcus faecium in a hospital system where resistance to daptomycin is evolving despite standard interventions. We hypothesized that the intravenous use of daptomycin generates off-target selection for resistance in transmissible gastrointestinal (carriage) populations of E. faecium. We performed a cohort study in which the daptomycin resistance of E. faecium isolated from rectal swabs from daptomycin-exposed patients was compared to a control group of patients exposed to linezolid, a drug with similar indications. In the daptomycin-exposed group, daptomycin resistance of E. faecium from the off-target population was on average 50% higher than resistance in the control group (n = 428 clones from 22 patients). There was also greater phenotypic diversity in daptomycin resistance within daptomycin-exposed patients. In patients where multiple samples over time were available, a wide variability in temporal dynamics were observed, from long-term maintenance of resistance to rapid return to sensitivity after daptomycin treatment stopped. Sequencing of isolates from a subset of patients supports the argument that selection occurs within patients. Our results demonstrate that off-target gastrointestinal populations rapidly respond to intravenous antibiotic exposure. Focusing on the off-target evolutionary dynamics may offer novel avenues to slow the spread of antibiotic resistance.

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