Evaluating the Impact of Population Bottlenecks in Experimental Evolution

Genetics ◽  
2002 ◽  
Vol 162 (2) ◽  
pp. 961-971 ◽  
Author(s):  
Lindi M Wahl ◽  
Philip J Gerrish ◽  
Ivan Saika-Voivod
Keyword(s):  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Population Bottlenecks ◽  
Dilution Ratio ◽  
Beneficial Mutation ◽  
Serial Transfer ◽  
Beneficial Mutations ◽  
Resource Limited ◽  
Total Fraction ◽  
The Impact

AbstractExperimental evolution involves severe, periodic reductions in population size when fresh media are inoculated during serial transfer. These bottlenecks affect the dynamics of evolution, reducing the probability that a beneficial mutation will reach fixation. We quantify the impact of these bottlenecks on the evolutionary dynamics, for populations that grow exponentially between transfers and for populations in which growth is curbed by a resource-limited environment. We find that in both cases, mutations that survive bottlenecks are equally likely to occur, per unit time, at all times during the growth phase. We estimate the total fraction of beneficial mutations that are lost due to bottlenecks during experimental evolution protocols and derive the “optimal” dilution ratio, the ratio that maximizes the number of surviving beneficial mutations. Although more severe dilution ratios are often used in the literature, we find that a ratio of 0.1-0.2 minimizes the chances that rare beneficial mutations are lost. Finally, we provide a number of useful approximate results and illustrate our approach with applications to experimental evolution protocols in the literature.

scholarly journals Effects of periodic bottlenecks on the dynamics of adaptive evolution in microbial populations

2021 ◽  
Author(s):  
Minako Izutsu ◽  
Devin M. Lake ◽  
Zachary W. D. Matson ◽  
Jack P. Dodson ◽  
Richard E. Lenski
Keyword(s):  
Simple Model ◽  
The Other ◽  
Population Bottlenecks ◽  
Final Size ◽  
Beneficial Mutations ◽  
Resource Limited ◽  
Long Term Experiment ◽  
The One ◽  
The Impact

Population bottlenecks are common in nature, and they can impact the rate of adaptation in evolving populations. On the one hand, each bottleneck reduces the genetic variation that fuels adaptation. On the other hand, fewer founders can undergo more generations and leave more descendants in a resource-limited environment, which allows surviving beneficial mutations to spread more quickly. Here we investigate the impact of repeated bottlenecks on the dynamics of adaptation in experimental populations of Escherichia coli. We propagated 48 populations under four dilution regimes (2-, 8-, 100-, and 1000-fold), all reaching the same final size each day, for 150 days. A simple model in which adaptation is limited by the supply rate of beneficial mutations predicts that fitness gains should be maximized with ~8-fold dilutions. The model also assumes that selection acts only on the overall growth rate and is otherwise identical across dilution regimes. However, we found that selection in the 2-fold regime was qualitatively different from the other treatments. Moreover, we observed earlier and greater fitness gains in the populations subjected to 100- and 1000-fold dilutions than in those that evolved in the 8 fold regime. We also ran simulations using parameters estimated independently from a long-term experiment using the same ancestral strain and environment. The simulations produced dynamics similar to our empirical results under these regimes, and they indicate that the simple model fails owing to the assumption that the supply of beneficial mutations limits adaptation.

scholarly journals Evolutionary dynamics and structural consequences of de novo beneficial mutations and mutant lineages arising in a constant environment

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Margie Kinnersley ◽  
Katja Schwartz ◽  
Dong-Dong Yang ◽  
Gavin Sherlock ◽  
Frank Rosenzweig
Keyword(s):  
High Frequency ◽  
High Throughput Sequencing ◽  
Evolutionary Dynamics ◽  
De Novo ◽  
Allelic Diversity ◽  
Microbial Evolution ◽  
De Novo Mutations ◽  
Beneficial Mutations ◽  
Adaptive Mutations ◽  
The Impact

Abstract Background Microbial evolution experiments can be used to study the tempo and dynamics of evolutionary change in asexual populations, founded from single clones and growing into large populations with multiple clonal lineages. High-throughput sequencing can be used to catalog de novo mutations as potential targets of selection, determine in which lineages they arise, and track the fates of those lineages. Here, we describe a long-term experimental evolution study to identify targets of selection and to determine when, where, and how often those targets are hit. Results We experimentally evolved replicate Escherichia coli populations that originated from a mutator/nonsense suppressor ancestor under glucose limitation for between 300 and 500 generations. Whole-genome, whole-population sequencing enabled us to catalog 3346 de novo mutations that reached > 1% frequency. We sequenced the genomes of 96 clones from each population when allelic diversity was greatest in order to establish whether mutations were in the same or different lineages and to depict lineage dynamics. Operon-specific mutations that enhance glucose uptake were the first to rise to high frequency, followed by global regulatory mutations. Mutations related to energy conservation, membrane biogenesis, and mitigating the impact of nonsense mutations, both ancestral and derived, arose later. New alleles were confined to relatively few loci, with many instances of identical mutations arising independently in multiple lineages, among and within replicate populations. However, most never exceeded 10% in frequency and were at a lower frequency at the end of the experiment than at their maxima, indicating clonal interference. Many alleles mapped to key structures within the proteins that they mutated, providing insight into their functional consequences. Conclusions Overall, we find that when mutational input is increased by an ancestral defect in DNA repair, the spectrum of high-frequency beneficial mutations in a simple, constant resource-limited environment is narrow, resulting in extreme parallelism where many adaptive mutations arise but few ever go to fixation.

scholarly journals Beneficial mutations and the dynamics of adaptation in asexual populations

2010 ◽  
Vol 365 (1544) ◽  
pp. 1255-1263 ◽  
Author(s):  
Paul D. Sniegowski ◽  
Philip J. Gerrish
Keyword(s):  
Experimental Evolution ◽  
Deterministic Model ◽  
Clonal Evolution ◽  
Empirical Support ◽  
Selection Model ◽  
Beneficial Mutation ◽  
Beneficial Mutations ◽  
Asexual Populations ◽  
Theoretical Results ◽  
Very High

We discuss the dynamics of adaptive evolution in asexual (clonal) populations. The classical ‘periodic selection’ model of clonal evolution assumed that beneficial mutations are very rare and therefore substitute unfettered into populations as occasional, isolated events. Newer models allow for the possibility that beneficial mutations are sufficiently common to coexist and compete for fixation within populations. Experimental evolution studies in microbes provide empirical support for stochastic models in which both selection and mutation are strong effects and clones compete for fixation; however, the relative importance of competition among clones bearing mutations of different selective effects versus competition among clones bearing multiple mutations remains unresolved. We provide some new theoretical results, moreover, suggesting that population dynamics consistent with the periodic selection model can arise even in a deterministic model that can accommodate a very high beneficial mutation rate.

scholarly journals Evaluating clinical outcomes of routinely delivered task-shared care for depression in rural Haiti

2021 ◽  
Vol 8 ◽  
Author(s):  
Alexandra L. Rose ◽  
Ryan McBain ◽  
Jesse Wilson ◽  
Sarah F. Coleman ◽  
Emmanuel Mathieu ◽  
...  
Keyword(s):  
Mental Health ◽  
Clinical Outcomes ◽  
Positive Impact ◽  
International Health ◽  
Routine Care ◽  
Care Organization ◽  
Depression Care ◽  
Resource Limited Settings ◽  
Resource Limited ◽  
The Impact

Abstract Background There is a growing literature in support of the effectiveness of task-shared mental health interventions in resource-limited settings globally. However, despite evidence that effect sizes are greater in research studies than actual care, the literature is sparse on the impact of such interventions as delivered in routine care. In this paper, we examine the clinical outcomes of routine depression care in a task-shared mental health system established in rural Haiti by the international health care organization Partners In Health, in collaboration with the Haitian Ministry of Health, following the 2010 earthquake. Methods For patients seeking depression care betw|een January 2016 and December 2019, we conducted mixed-effects longitudinal regression to quantify the effect of depression visit dose on symptoms, incorporating interaction effects to examine the relationship between baseline severity and dose. Results 306 patients attended 2052 visits. Each visit was associated with an average reduction of 1.11 in depression score (range 0–39), controlling for sex, age, and days in treatment (95% CI −1.478 to −0.91; p < 0.001). Patients with more severe symptoms experienced greater improvement as a function of visits (p = 0.04). Psychotherapy was provided less frequently and medication more often than expected for patients with moderate symptoms. Conclusions Our findings support the potential positive impact of scaling up routine mental health services in low- and middle-income countries, despite greater than expected variability in service provision, as well as the importance of understanding potential barriers and facilitators to care as they occur in resource-limited settings.

scholarly journals The impact of death and dying on the personhood of medical students: a systematic scoping review

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Chong Yao Ho ◽  
Cheryl Shumin Kow ◽  
Chin Howe Joshua Chia ◽  
Jia Ying Low ◽  
Yong Hao Melvin Lai ◽  
...  
Keyword(s):  
Medical Students ◽  
Scoping Review ◽  
Death And Dying ◽  
Support Mechanism ◽  
Resource Limited ◽  
Dying Patients ◽  
Concurrent Use ◽  
Effective Training ◽  
Longitudinal Support ◽  
The Impact

Abstract Background The re-introduction of medical students into healthcare systems struggling with the COVID-19 pandemic raises concerns as to whether they will be supported when confronted with death and dying patients in resource-limited settings and with reduced support from senior clinicians. Better understanding of how medical students respond to death and dying will inform educationalists and clinicians on how to best support them. Methods We adopt Krishna’s Systematic Evidence Based Approach to carry out a Systematic Scoping Review (SSR in SEBA) on the impact of death and dying on medical students. This structured search process and concurrent use of thematic and directed content analysis of data from six databases (Split Approach) enhances the transparency and reproducibility of this review. Results Seven thousand six hundred nineteen were identified, 149 articles reviewed and 52 articles included. The Split Approach revealed similar themes and categories that correspond to the Innate, Individual, Relational and Societal domains in the Ring Theory of Personhood. Conclusion Facing death and dying amongst their patients affect how medical students envisage their personhood. This underlines the need for timely, holistic and longitudinal support systems to ensure that problems faced are addressed early. To do so, there must be effective training and a structured support mechanism.

scholarly journals The importance of species interactions in eco-evolutionary community dynamics under climate change

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Anna Åkesson ◽  
Alva Curtsdotter ◽  
Anna Eklöf ◽  
Bo Ebenman ◽  
Jon Norberg ◽  
...  
Keyword(s):  
Climate Change ◽  
Species Interactions ◽  
Community Dynamics ◽  
Evolutionary Dynamics ◽  
Negative Impact ◽  
Trophic Levels ◽  
Temperature Dependent ◽  
Modeling Framework ◽  
Impact Of Climate Change ◽  
The Impact

AbstractEco-evolutionary dynamics are essential in shaping the biological response of communities to ongoing climate change. Here we develop a spatially explicit eco-evolutionary framework which features more detailed species interactions, integrating evolution and dispersal. We include species interactions within and between trophic levels, and additionally, we incorporate the feature that species’ interspecific competition might change due to increasing temperatures and affect the impact of climate change on ecological communities. Our modeling framework captures previously reported ecological responses to climate change, and also reveals two key results. First, interactions between trophic levels as well as temperature-dependent competition within a trophic level mitigate the negative impact of climate change on biodiversity, emphasizing the importance of understanding biotic interactions in shaping climate change impact. Second, our trait-based perspective reveals a strong positive relationship between the within-community variation in preferred temperatures and the capacity to respond to climate change. Temperature-dependent competition consistently results both in higher trait variation and more responsive communities to altered climatic conditions. Our study demonstrates the importance of species interactions in an eco-evolutionary setting, further expanding our knowledge of the interplay between ecological and evolutionary processes.

scholarly journals Somatic deficiency causes reproductive parasitism in a fungus

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Alexey A. Grum-Grzhimaylo ◽  
Eric Bastiaans ◽  
Joost van den Heuvel ◽  
Cristina Berenguer Millanes ◽  
Alfons J. M. Debets ◽  
...  
Keyword(s):  
Neurospora Crassa ◽  
Experimental Evolution ◽  
Evolutionary Dynamics ◽  
Genetic Load ◽  
Wild Type ◽  
Fusion Frequency ◽  
Somatic Fusion ◽  
Extensive Variation ◽  
Reproductive Parasitism ◽  
Multicellular Organisms

AbstractSome multicellular organisms can fuse because mergers potentially provide mutual benefits. However, experimental evolution in the fungus Neurospora crassa has demonstrated that free fusion of mycelia favours cheater lineages, but the mechanism and evolutionary dynamics of this exploitation are unknown. Here we show, paradoxically, that all convergently evolved cheater lineages have similar fusion deficiencies. These mutants are unable to initiate fusion but retain access to wild-type mycelia that fuse with them. This asymmetry reduces cheater-mutant contributions to somatic substrate-bound hyphal networks, but increases representation of their nuclei in the aerial reproductive hyphae. Cheaters only benefit when relatively rare and likely impose genetic load reminiscent of germline senescence. We show that the consequences of somatic fusion can be unequally distributed among fusion partners, with the passive non-fusing partner profiting more. We discuss how our findings may relate to the extensive variation in fusion frequency of fungi found in nature.

scholarly journals Genome context influences evolutionary flexibility of nearly identical type III effectors in two phytopathogenic Pseudomonads

2021 ◽  
Author(s):  
David A Baltrus ◽  
Qian Feng ◽  
Brian H Kvitko
Keyword(s):  
Pseudomonas Syringae ◽  
Evolutionary Dynamics ◽  
Effector Proteins ◽  
In Planta ◽  
Genomic Context ◽  
Type Iii Effectors ◽  
Type Iii ◽  
Genome Context ◽  
The Impact ◽  
Multiple Type

Integrative Conjugative Elements (ICEs) are replicons that can insert and excise from chromosomal locations in a site specific manner, can conjugate across strains, and which often carry a variety of genes useful for bacterial growth and survival under specific conditions. Although ICEs have been identified and vetted within certain clades of the agricultural pathogen Pseudomonas syringae, the impact of ICE carriage and transfer across the entire P. syringae species complex remains underexplored. Here we identify and vet an ICE (PmaICE-DQ) from P. syringae pv. maculicola ES4326, a strain commonly used for laboratory virulence experiments, demonstrate that this element can excise and conjugate across strains, and contains loci encoding multiple type III effector proteins. Moreover, genome context suggests that another ICE (PmaICE-AOAB) is highly similar in comparison with and found immediately adjacent to PmaICE-DQ within the chromosome of strain ES4326, and also contains multiple type III effectors. Lastly, we present passage data from in planta experiments that suggests that genomic plasticity associated with ICEs may enable strains to more rapidly lose type III effectors that trigger R-gene mediated resistance in comparison to strains where nearly isogenic effectors are not present in ICEs. Taken together, our study sheds light on a set of ICE elements from P. syringae pv. maculicola ES4326 and highlights how genomic context may lead to different evolutionary dynamics for shared virulence genes between strains.

scholarly journals The Genomic Ecosystem of Transposable Elements in Maize

2019 ◽  
Author(s):  
Michelle C. Stitzer ◽  
Sarah N. Anderson ◽  
Nathan M. Springer ◽  
Jeffrey Ross-Ibarra
Keyword(s):  
Transposable Elements ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Flowering Plant ◽  
Genome Wide ◽  
Family Level ◽  
Genomic Environment ◽  
Single Category ◽  
The Impact

Transposable elements (TEs) constitute the majority of flowering plant DNA, reflecting their tremendous success in subverting, avoiding, and surviving the defenses of their host genomes to ensure their selfish replication. More than 85% of the sequence of the maize genome can be ascribed to past transposition, providing a major contribution to the structure of the genome. Evidence from individual loci has informed our understanding of how transposition has shaped the genome, and a number of individual TE insertions have been causally linked to dramatic phenotypic changes. But genome-wide analyses in maize and other taxa have frequently represented TEs as a relatively homogeneous class of fragmentary relics of past transposition, obscuring their evolutionary history and interaction with their host genome. Using an updated annotation of structurally intact TEs in the maize reference genome, we investigate the family-level ecological and evolutionary dynamics of TEs in maize. Integrating a variety of data, from descriptors of individual TEs like coding capacity, expression, and methylation, as well as similar features of the sequence they inserted into, we model the relationship between these attributes of the genomic environment and the survival of TE copies and families. Our analyses reveal a diversity of ecological strategies of TE families, each representing the evolution of a distinct ecological niche allowing survival of the TE family. In contrast to the wholesale relegation of all TEs to a single category of junk DNA, these differences generate a rich ecology of the genome, suggesting families of TEs that coexist in time and space compete and cooperate with each other. We conclude that while the impact of transposition is highly family- and context-dependent, a family-level understanding of the ecology of TEs in the genome can refine our ability to predict the role of TEs in generating genetic and phenotypic diversity.‘Lumping our beautiful collection of transposons into a single category is a crime’-Michael R. Freeling, Mar. 10, 2017

Sign in / Sign up

Export Citation Format

Share Document