Evolutionary contribution to coexistence of competitors in microbial food webs

The theory of species coexistence is a key concept in ecology that has received much attention. The role of rapid evolution for determining species coexistence is still poorly understood although evolutionary change on ecological time-scales has the potential to change almost any ecological process. The influence of evolution on coexistence can be especially pronounced in microbial communities where organisms often have large population sizes and short generation times. Previous work on coexistence has assumed that traits involved in resource use and species interactions are constant or change very slowly in terms of ecological time-scales. However, recent work suggests that these traits can evolve rapidly. Nevertheless, the importance of rapid evolution to coexistence has not been tested experimentally. Here, we show how rapid evolution alters the frequency of two bacterial competitors over time when grown together with specialist consumers (bacteriophages), a generalist consumer (protozoan) and all in combination. We find that consumers facilitate coexistence in a manner consistent with classic ecological theory. However, through disentangling the relative contributions of ecology (changes in consumer abundance) and evolution (changes in traits mediating species interactions) on the frequency of the two competitors over time, we find differences between the consumer types and combinations. Overall, our results indicate that the influence of evolution on species coexistence strongly depends on the traits and species interactions considered.

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Competition between continuously evolving lineages in asexual populations

10.1101/062976 ◽

2016 ◽

Author(s):

Noah Ribeck ◽

Joseph S. Mulka ◽

Luis Zaman ◽

Brian D. Connelly ◽

Richard E. Lenski

Keyword(s):

Large Population ◽

Current Theory ◽

Simple Expression ◽

Critical Threshold ◽

Beneficial Mutation ◽

Asexual Population ◽

Simplifying Assumptions ◽

Population Sizes ◽

Asexual Populations

ABSTRACTIn an asexual population, the fate of a beneficial mutation depends on how its lineage competes against other mutant lineages in the population. With high beneficial mutation rates or large population sizes, competition between contending mutations is strong, and successful lineages can accumulate multiple mutations before any single one achieves fixation. Most current theory about asexual population dynamics either neglects this multiple-mutations regime or introduces simplifying assumptions that may not apply. Here, we develop a theoretical framework that describes the dynamics of adaptation and substitution over all mutation-rate regimes by conceptualizing the population as a collection of continuously adapting lineages. This model of “lineage interference” shows that each new mutant’s advantage over the rest of the population must be above a critical threshold in order to likely achieve fixation, and we derive a simple expression for that threshold. We apply this framework to examine the role of beneficial mutations with different effect sizes across the transition to the multiple-mutations regime.

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Predictions of response to artificial selection from new mutations

Genetics Research ◽

10.1017/s0016672300019145 ◽

1982 ◽

Vol 40 (3) ◽

pp. 255-278 ◽

Cited By ~ 100

Author(s):

William G. Hill

Keyword(s):

Large Population ◽

Mutant Gene ◽

Gene Effects ◽

Bristle Number ◽

Large Populations ◽

Breeding Programmes ◽

Population Sizes ◽

The Difference ◽

Mutant Genes

SUMMARYThe pattern of response expected from fixation of mutant genes for quantitative traits in finite populations is investigated for a range of distributions of mutant gene effects. The eventual rate depends on the total variance of mutant effects per generation, but the initial rate and the variance of response is higher if the distribution of mutant effects has a large standard deviation or is leptokurtic. The difference between initial and eventual rates of response is greater with large population sizes.For a range of assumptions, new mutants are unlikely to have much influence on response for 20 or so generations, but then may contribute substantially, such that no plateaux are obtained. However, information on the variance contributed by mutants is almost entirely on bristle number in Drosophila.It is argued that the role of new mutants should be considered in designing breeding programmes, in particular in utilizing large populations.

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Ploidy and the evolution of parasitism

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2010.2146 ◽

2011 ◽

Vol 278 (1719) ◽

pp. 2814-2822 ◽

Cited By ~ 11

Author(s):

Leithen K. M'Gonigle ◽

Sarah P. Otto

Keyword(s):

Ploidy Level ◽

Species Interactions ◽

Finite Population ◽

Genetic Model ◽

Multiple Alleles ◽

Generation Times ◽

Population Sizes ◽

Genetic Mechanisms ◽

Host Parasite ◽

The Continuum

Levels of parasitism are continuously distributed in nature. Models of host–parasite coevolution, however, typically assume that species can be easily characterized as either parasitic or non-parasitic. Consequently, it is poorly understood which factors influence the evolution of parasitism itself. We investigate how ploidy level and the genetic mechanisms underlying infection influence evolution along the continuum of parasitism levels. In order for parasitism to evolve, selective benefits to the successful invasion of hosts must outweigh the losses when encountering resistant hosts. However, we find that exactly where this threshold occurs depends not only on the strength of selection, but also on the genetic model of interaction, the ploidy level in each species, and the nature of the costs to virulence and resistance. With computer simulations, we are able to incorporate more realistic dynamics at the loci underlying species interactions and to extend our analyses in a number of directions, including finite population sizes, multiple alleles and different generation times.

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Quantifying the impacts of human mobility restriction on the spread of COVID-19: an empirical analysis from 344 cities of China

10.1101/2020.07.13.20148668 ◽

2020 ◽

Author(s):

Jing Tan ◽

Yiquan Xiong ◽

Shaoyang Zhao ◽

Chunrong Liu ◽

Shiyao Huang ◽

...

Keyword(s):

Human Mobility ◽

Large Population ◽

Disease Spread ◽

Population Mobility ◽

Population Sizes ◽

The Difference ◽

Novel Coronavirus ◽

The Impact ◽

The City ◽

Over Time

AbstractObjectiveSince the outbreak of novel coronavirus pneumonia (COVID-19), human mobility restriction measures have raised controversies, partly due to inconsistent findings. Empirical study is urgently needed to reliably assess the causal effects of mobility restriction.MethodsOur study applied the difference-in-difference (DID) model to assess declines of population mobility at the city level, and used the log-log regression model to examine the effects of population mobility declines on the disease spread measured by cumulative or new cases of COVID-19 over time, after adjusting for confounders.ResultsThe DID model showed that a continual expansion of the relative declines over time in 2020. After four weeks, population mobility declined by 54.81% (interquartile ranges, −65.50% to −43.56%). The accrued population mobility declines were associated with significant reduction of cumulative COVID-19 cases throughout six weeks (i.e., 1% decline of population mobility was associated with 0.72% (95%CI 0.50% to 0.93%) reduce of cumulative cases for one week, 1.42% two weeks, 1.69% three weeks, 1.72% four weeks,1.64% five weeks and 1.52% six weeks). The impact on weekly new cases seemed greater in the first four weeks, but faded thereafter. The effects on cumulative cases differed by cities of different population sizes, with greater effects seen in larger cities.ConclusionPersistent population mobility restrictions are well deserved. However, a change in the degree of mobility restriction may be warranted over time, particularly after several weeks of rigorous mobility restriction. Implementation of mobility restrictions in major cities with large population sizes may be even more important.

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Deficits in decision-making induced by parietal cortex inactivation are compensated at two time scales

10.1101/2021.09.10.459856 ◽

2021 ◽

Author(s):

Danique Jeurissen ◽

S Shushruth ◽

Yasmine El-Shamayleh ◽

Gregory D Horwitz ◽

Michael N Shadlen

Keyword(s):

Decision Making ◽

Working Memory ◽

Time Scales ◽

Brain Function ◽

Rhesus Monkeys ◽

Experimental Session ◽

Cortical Circuits ◽

Lateral Intraparietal Area ◽

Over Time

AbstractPerceptual decisions arise through the transformation of samples of evidence into a commitment to a proposition or plan of action. Such transformation is thought to involve cortical circuits capable of computation over time scales associated with working memory, attention, and planning. Neurons in the lateral intraparietal area (LIP) are thought to play a role in all of these functions, and much of what is known about the neurobiology of decision making has been influenced by studies of LIP and its network of cortical and subcortical connections. However a causal role of neurons in LIP remains controversial. We used pharmacological and chemogenetic methods to inactivate LIP in one hemisphere of four rhesus monkeys. Inactivation produced clear biases in decisions, but the effects dissipated despite the persistence of neural inactivation, implying compensation by other unaffected areas. Compensation occurs on a rapid times scale, within an experimental session, and more gradually, across sessions. The findings resolve disparate studies and inform interpretation of focal perturbations of brain function.

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Abstract WP30: Trends and Outcomes of Endovascular Revascularization Therapy for the ASIAN KR Registry

Stroke ◽

10.1161/str.48.suppl_1.wp30 ◽

2017 ◽

Vol 48 (suppl_1) ◽

Author(s):

Yang-Ha Hwang ◽

Yong-Won Kim ◽

Jeong-Ho Hong ◽

Chang-Hyun Kim ◽

Hyuk Won Chang ◽

...

Keyword(s):

Ischemic Stroke ◽

Clinical Outcome ◽

Acute Ischemic Stroke ◽

Rapid Evolution ◽

Favorable Outcome ◽

Anterior Circulation ◽

Revascularization Therapy ◽

Multicenter Registry ◽

Over Time

Background and Purpose: The rapid evolution of endovascular therapy (EVT) in acute ischemic stroke has benefited its performance in real clinical practice. The aim of this study is to describe the annual trends of EVT performance after the introduction of the stentriever in Korea. Methods: Data were retrospectively collected from the ASIAN KR (Acute Stroke due to Intracranial Atherosclerotic occlusion and Neurointervention - Korean Retrospective) registry between January 2011 and December 2015. The ASIAN KR registry is an observational multicenter registry of consecutive patients treated with EVT for acute ischemic stroke. Trends in EVT performance were described and analyzed. Results: A total of 649 patients were included for analysis. The target arterial occlusive lesions included 584 in the anterior circulation (including 158 ICA terminuses and 293 MCA M1s) and 65 in the posterior circulation. Overall, successful reperfusion (mTICI 2b-3, post-procedure) and favorable outcome (mRS 0-2 or equal to prestroke mRS, at 3-month) was achieved in 500 patients (77.0%) and 332 patients (51.2%), respectively. A trend for increase in successful reperfusion and favorable outcome over time was observed (73.9% in 2011 vs. 83.1% in 2015, p =0.040; 48.7% in 2011 vs. 58.1% in 2015, p =0.074). Utilization of a stentriever as a first-chosen device for EVT increased over time from 12.8% in 2011 to 46.9% in 2015 ( p <0.001). This was accompanied by a significant trend for shorter time regarding arrival to groin puncture and groin puncture to end of EVT procedure (median 119 minutes in 2011 vs. 86 minutes in 2015, p <0.001; 68 minutes in 2011 vs. 54.5 minutes in 2015, p <0.001). After adjustment for age, onset to groin puncture time, and successful reperfusion, a trend for better clinical outcome over time following EVT remained statistically significant (odds ratio 1.13, 95% CI 1.01-1.27; p =0.033) Conclusions: A upward trend in successful reperfusion and better clinical outcome was observed along with improvement in intra-hospital workflow and utilization of up-to-date thrombectomy devices over time, which emphasizes the role of EVT experience, quality improvement of workflow, and use of newer EVT devices.

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Outcomes of Previously Untreated Older Patients with Multiple Myeloma (MM) over Time: An Analysis of 3 Consecutive Trials Conducted by the NCIC CTG, 1983–2003.

Blood ◽

10.1182/blood.v106.11.2568.2568 ◽

2005 ◽

Vol 106 (11) ◽

pp. 2568-2568

Author(s):

Cynthia Luk ◽

Keyue Ding ◽

Andrew R. Belch ◽

George P. Browman ◽

Chaim Shustik ◽

...

Keyword(s):

Multivariate Analyses ◽

Large Population ◽

Progression Free Survival ◽

Random Allocation ◽

Baseline Serum ◽

Free Survival ◽

Baseline Characteristics ◽

Ecog Ps ◽

Over Time

Abstract Background: Improved overall survival (OS) over time has been observed in large population databases assessing patients (pts) with MM. Recent interventions, such as routine use of bisphosphonates, and stem cell transplantation for younger pts may account for some of this improvement. It is unclear whether these improvements have been seen in older symptomatic pts. The purpose of this study is to assess outcomes over time of pts > 65 yrs with MM who were entered on 3 consecutive randomized trials conducted by NCIC CTG. Methods: Databases evaluated included MY4 (1983–84; N=173), which compared etidronate to placebo; MY6 (1987–92; N=402), which tested the role of maintenance interferon; and MY7 (1995–2003; N=584), which tested dexamethasone as induction and maintenance therapy. All pts had symptomatic Salmon-Durie stage I or stage II–III MM, were previously untreated, and received melphalan 9 mg/M2 and prednisone 100 mg daily x 4, Q4 weeks; 231 pts in MY7 received melphalan and dexamethasone according to random allocation. We performed uni- and multivariate analyses to compare outcomes of pts ≤ 65 and > 65 yrs of age, to assess outcomes of pts > 65 yrs over time, and to assess other prognostic determinants in pts > 65 yrs. Outcomes of interest included OS, progression-free survival (PFS), myeloma-related survival (MRS), defined as time from registration or randomization until death from myeloma or treatment toxicity, and time from first progression to death (FPTD). Results: All eligible pts were included. By multivariate analyses, patients > 65 yrs had inferior OS (p=0.0003), FPTD (p=0.0006), and a trend for inferior MRS (p=0.08) in comparison with pts ≤ 65 yrs; no difference in PFS was detected. In comparing pts >65 yrs on MY4, MY6 and MY7, important differences in the baseline characteristics of the patients of the 3 trials were noted; pts treated on MY6 received lower median cumulative doses of melphalan (356 mg/M2) than those entered on to MY4 (432 mg/M2) or MY-7 (464 mg/M2). Median unadjusted outcomes of these pts by trial are listed in the table below. By multivariate analysis, pts > 65 yrs entered on to MY4 had a superior MRS in comparison with MY7 (p=0.037) and a trend to superior OS (p=0.053) and FPTD (p=0.06). No differences in PFS between trials were detected. Baseline characteristics associated with inferior OS in pts > 65 yrs included ECOG PS > 1 (p=0.0002), male gender (p=0.001), baseline Hb ≤ 85 g/L (p=0.001), and elevated baseline serum calcium (p=0.01). Conclusions: Patients > 65 yrs have inferior outcomes in comparison with younger pts. We were unable to detect improvements in outcomes of these pts over time. Median unadjusted outcomes of pts age > 65 yrs by trial MY4 (95% CI) MY6 (95% CI) MY7 (95% CI) OS (yrs) 2.38 (1.73–3.32) 2.75 (2.36–3.24) 2.53 (2.32–2.75) PFS (yrs) 1.00 (0.90–1.41) 1.53 (1.38–1.75) 1.80 (1.61–1.92) MRS (yrs) 2.98 (1.78–3.59) 3.30 (2.66–3.79) 2.90 (2.61–3.22) FPTD (yrs) 1.21 (0.76–1.91) 1.27 (0.84–2.02) 0.85 (0.68–1.07)

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Microbial experimental evolution

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.90562.2008 ◽

2009 ◽

Vol 297 (1) ◽

pp. R17-R25 ◽

Cited By ~ 19

Author(s):

Albert F. Bennett ◽

Bradley S. Hughes

Keyword(s):

Experimental Evolution ◽

Large Scale ◽

Large Population ◽

Competitive Fitness ◽

Experimental Feature ◽

Generation Times ◽

Evolutionary Studies ◽

Direct Competition ◽

Population Sizes ◽

Experimental Subjects

Microbes have been widely used in experimental evolutionary studies because they possess a variety of valuable traits that facilitate large-scale experimentation. Many replicated populations can be cultured in the laboratory simultaneously along with appropriate controls. Short generation times and large population sizes make microbes ideal experimental subjects, ensuring that many spontaneous mutations occur every generation and that adaptive variants can spread rapidly through a population. Another highly useful experimental feature is the ability to preserve and store ancestral and evolutionarily derived clones. These can be revived in parallel to allow the direct measurement of the competitive fitness of a descendant compared with its ancestor. The extent of adaptation can thereby be measured quantitatively and compared statistically by direct competition among derived groups and with the ancestor. Thus, fitness and adaptation need not be matters of qualitative speculation, but are quantitatively measurable variables in these systems. Replication allows the quantification of heterogeneity in responses to imposed selection and thereby statistical distinction between changes that are systematic responses to the selective regimen and those that are specific to individual populations.

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