scholarly journals Evolution with a seed bank: the population genetic consequences of microbial dormancy

2017 ◽  
Author(s):  
WR Shoemaker ◽  
JT Lennon
Keyword(s):  
Seed Bank ◽  
Population Genetic ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Seed Banks ◽  
Hedging Strategy ◽  
Term Survival ◽  
Evolutionary Forces ◽  
Growth And Reproduction

ABSTRACTDormancy is a bet-hedging strategy that allows organisms to persist through conditions that are sub-optimal for growth and reproduction by entering a reversible state of reduced metabolic activity. Dormancy allows a population to maintain a reservoir of genetic and phenotypic diversity (i.e., a seed bank) that can contribute to the long-term survival of a population. This strategy can be potentially adaptive and has long been of interest to ecologists and evolutionary biologists. However, comparatively little is known about how dormancy influences the fundamental evolutionary forces of genetic drift, mutation, selection, recombination, and gene flow. Here, we investigate how seed banks affect the processes underpinning evolution by reviewing existing theory, implementing novel simulations, and determining how and when dormancy can influence evolution as a population genetic process. We extend our analysis to examine how seed banks can alter macroevolutionary processes, including rates of speciation and extinction. Through the lens of population genetic theory, we can understand the extent that seed banks influence microbial evolutionary dynamics.

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 The evolution of genetic diversity in changing environments

2014 ◽  
Author(s):  
Oana Carja ◽  
Uri Liberman ◽  
Marcus W. Feldman
Keyword(s):  
Phenotypic Variation ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Theoretical Models ◽  
Fluctuating Selection ◽  
Evolutionary Forces ◽  
And Migration ◽  
Compare And Contrast ◽  
Insight Into

The production and maintenance of genetic and phenotypic diversity under temporally fluctuating selection and the signatures of environmental and selective volatility in the patterns of genetic and phenotypic variation have been important areas of focus in population genetics. On one hand, stretches of constant selection pull the genetic makeup of populations towards local fitness optima. On the other, in order to cope with changes in the selection regime, populations may evolve mechanisms that create a diversity of genotypes. By tuning the rates at which variability is produced, such as the rates of recombination, mutation or migration, populations may increase their long-term adaptability. Here we use theoretical models to gain insight into how the rates of these three evolutionary forces are shaped by fluctuating selection. We compare and contrast the evolution of recombination, mutation and migration under similar patterns of environmental change and show that these three sources of phenotypic variation are surprisingly similar in their response to changing selection. We show that knowing the shape, size, variance and asymmetry of environmental runs is essential for accurate prediction of genetic evolutionary dynamics.

scholarly journals Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

2019 ◽  
Author(s):  
Kathryn E. Holt ◽  
Florent Lassalle ◽  
Kelly L. Wyres ◽  
Ryan Wick ◽  
Rafal J. Mostowy
Keyword(s):  
Evolutionary Dynamics ◽  
Bacterial Species ◽  
Purifying Selection ◽  
Evolutionary Forces ◽  
Polysaccharide Synthesis ◽  
Surface Polysaccharides ◽  
Surface Polysaccharide ◽  
Selective Preservation ◽  
Multiple Species

Bacterial capsules and lipopolysaccharides are diverse surface polysaccharides (SPs) that serve as the frontline for interactions with the outside world. While SPs can evolve rapidly, their diversity and evolutionary dynamics across different taxonomic scales has not been investigated in detail. Here, we focused on the bacterial order Enterobacteriales (including the medically-relevant Enterobacteriaceae), to carry out comparative genomics of two SP locus synthesis regions, cps and kps, using 27,334 genomes from 45 genera. We identified high-quality cps loci in 22 genera and kps in 11 genera, around 4% of which were detected in multiple species. We found SP loci to be highly dynamic genetic entities: their evolution was driven by high rates of horizontal gene transfer (HGT), both of whole loci and component genes, and relaxed purifying selection, yielding large repertoires of SP diversity. In spite of that, we found the presence of (near-)identical locus structures in distant taxonomic backgrounds that could not be explained by recent exchange, pointing to long-term selective preservation of locus structures in some populations. Our results reveal differences in evolutionary dynamics driving SP diversity within different bacterial species, with lineages of Escherichia coli, Enterobacter hormachei and Klebsiella aerogenes most likely to share SP loci via recent exchange; and lineages of Salmonella enterica, Citrobacter sakazakii and Serratia marcescens most likely to share SP loci via other mechanisms such as long-term preservation. Overall, the evolution of SP loci in Enterobacteriales is driven by a range of evolutionary forces and their dynamics and relative importance varies between different species.

Tagging experiments with western king prawn Penaeus latisculatus Kishinouye. I. Survival, growth, and reproduction of tagged prawns

1975 ◽  
Vol 26 (2) ◽  
pp. 197 ◽  
Author(s):  
JW Penn
Keyword(s):  
Western Australia ◽  
Ovary Development ◽  
Normal Ovary ◽  
Variable Amount ◽  
Physical Damage ◽  
Term Survival ◽  
Long Term Survival ◽  
Average Control ◽  
Growth And Reproduction

Two tags for adult western king prawns, Penaeus latisulcatus, have been field tested in an unexploited king prawn population in Cockburn Sound, Western Australia. Both toggle and Atkin tags have been found to cause little physical damage to the prawns apart from limited scarring at the points of entry and through the musculature adjacent to the tag. Long-term survival of both toggle- and Atkin-tagged prawns did not differ significantly from that of the untagged population, but a variable amount of initial tagging mortality occurred during the first 72 h after release due to both handling and tagging. Mortality related to size or sex was not evident for the toggle tags, but for Atkin tags there was a tendency towards smaller prawns having a better survival. Growth of all tagged prawns was found to be retarded during the first month from release, but in subsequent months appeared to be faster than the average control animals. Although the growth of tagged prawns recaptured during the spawning season was retarded, normal ovary development occurred and some females spawned while tagged. Some of the problems in the use of tag recapture data from penaeid prawn stocks have been discussed.

scholarly journals Oscillatory dynamics in a bacterial cross-protection mutualism

2016 ◽  
Vol 113 (22) ◽  
pp. 6236-6241 ◽  
Author(s):  
Eugene Anatoly Yurtsev ◽  
Arolyn Conwill ◽  
Jeff Gore
Keyword(s):  
Evolutionary Dynamics ◽  
Cooperative Behavior ◽  
Cross Protection ◽  
Common Mechanism ◽  
Natural Environments ◽  
Term Survival ◽  
Bacterial Populations ◽  
Oscillatory Dynamics ◽  
Protection Mutualism

Cooperation between microbes can enable microbial communities to survive in harsh environments. Enzymatic deactivation of antibiotics, a common mechanism of antibiotic resistance in bacteria, is a cooperative behavior that can allow resistant cells to protect sensitive cells from antibiotics. Understanding how bacterial populations survive antibiotic exposure is important both clinically and ecologically, yet the implications of cooperative antibiotic deactivation on the population and evolutionary dynamics remain poorly understood, particularly in the presence of more than one antibiotic. Here, we show that two Escherichia coli strains can form an effective cross-protection mutualism, protecting each other in the presence of two antibiotics (ampicillin and chloramphenicol) so that the coculture can survive in antibiotic concentrations that inhibit growth of either strain alone. Moreover, we find that daily dilutions of the coculture lead to large oscillations in the relative abundance of the two strains, with the ratio of abundances varying by nearly four orders of magnitude over the course of the 3-day period of the oscillation. At modest antibiotic concentrations, the mutualistic behavior enables long-term survival of the oscillating populations; however, at higher antibiotic concentrations, the oscillations destabilize the population, eventually leading to collapse. The two strains form a successful cross-protection mutualism without a period of coevolution, suggesting that similar mutualisms may arise during antibiotic treatment and in natural environments such as the soil.

Depauperate seed banks in urban tropical seagrass meadows

2020 ◽  
Vol 71 (8) ◽  
pp. 935
Author(s):  
Glendon Hong Ming Ong ◽  
Samantha Lai ◽  
Siti Maryam Yaakub ◽  
Peter Todd
Keyword(s):  
Seed Bank ◽  
Large Scale ◽  
Seed Viability ◽  
Seed Banks ◽  
Dormant Seed ◽  
Seagrass Meadows ◽  
Halophila Ovalis ◽  
The Status ◽  
Cymodocea Rotundata

Seagrasses need to be resilient if they are to persist in the long term. Being able to build up a dormant seed bank in sediments is a key strategy that some species employ to regenerate from large-scale degradation. Much of the research on seed banks has focussed on temperate species, and little is known regarding the status of seed banks in tropical meadows. In the present study, we examined the seed bank status of three common seagrass species at six sites in Singapore and attempted to identify potential drivers of seed abundance. Our results indicated depauperate seed banks with few species setting viable seed and low seed densities. Halophila ovalis seeds were found at four sites and Halodule uninervis seeds at two sites, but Cymodocea rotundata seeds were absent from all six sites. Whereas H. ovalis seed viability ranged from 20% to 68.8%, none of the H. uninervis seeds was viable. Halophila ovalis seed densities (33–334m–2) were much higher than those of H. uninervis (9–21m–2). Of the variables examined, only H. ovalis cover was positively correlated with the number of seeds. Our study has highlighted the vulnerability of seagrass meadows in Singapore’s urban waters to future disturbances.

Germination requirements of Oenothera biennis seeds during burial under natural seasonal temperature cycles

1994 ◽  
Vol 72 (6) ◽  
pp. 779-782 ◽  
Author(s):  
Carol C. Baskin ◽  
Jerry M. Baskin
Keyword(s):  
Seed Banks ◽  
Late Winter ◽  
Seasonal Temperature ◽  
Oenothera Biennis ◽  
Light Requirement ◽  
Term Survival ◽  
Temperature Changes ◽  
Buried Seeds ◽  
Dormancy Cycles

Buried seeds of Oenothera biennis, which have the potential to form long-lived seed banks, were investigated to determine whether or not they (i) undergo seasonal changes in their dormancy states and (ii) require light for germination. Seeds were buried in soil and exposed to natural seasonal temperature changes. Samples of seeds were exhumed at monthly intervals for 31 months and tested for germination in light and darkness at 12-h daily thermoperiods of 15:6, 20:10, 25:15, 30:15, and 35:20 °C. At maturity in autumn, seeds germinated to 84–95% in light at 30:15 and 35:20 °C, but to 0–69% at other test conditions. By late winter, seeds germinated to 95–100% at the five thermoperiods in light and in darkness. In summer and autumn, germination in light decreased at 15:6 °C, and in darkness it dropped to 0% at 15:6 °C and decreased at 20:10, 25:15, 30:15, and 35:20 °C. Following the second winter of burial, seeds germinated to near 100% at all thermoperiods in light and darkness. Thus, seeds exhibited an annual nondormancy – conditional dormancy cycle, being nondormant from midwinter to late spring and conditionally dormant in summer and autumn. Oenothera biennis is 1 of 10 species whose seeds live for 39–40 years or longer in soil and also have an annual conditional dormancy – nondormancy cycle. Seeds of six of these species, including O. biennis, can germinate in darkness in spring or summer at simulated habitat temperatures. Therefore, a light requirement for germination is not necessarily a prerequisite for long-term survival of buried seeds, and something other than darkness prevents germination of seeds of some species buried in soil. Key words: seed banks, buried seeds, germination, dormancy cycles, light requirement, Oenothera.

scholarly journals Ecological memory preserves phage resistance mechanisms in bacteria

2020 ◽  
Author(s):  
Antun Skanata ◽  
Edo Kussell
Keyword(s):  
Evolutionary Biology ◽  
Defense Mechanisms ◽  
Evolutionary Dynamics ◽  
Resistance Mechanisms ◽  
Term Survival ◽  
Linear Dynamical Systems ◽  
Ecological Memory ◽  
Wide Range ◽  
The Face

Defense mechanisms against pathogens are prevalent in nature, and their maintenance is critical for long-term survival of a species. Such mechanisms, which include CRISPR-mediated immunity in bacteria and the R genes in plants, carry substantial costs to organisms and can be rapidly lost when pathogens are eliminated. How a species preserves its molecular defenses despite their costs, in the face of variable pathogen levels, and across an ecology of localized patches remains a major unsolved problem in epidemiology and evolutionary biology. Using techniques of game theory and non-linear dynamical systems, we show that by maintaining a non-zero failure rate of immunity, hosts sustain sufficient levels of pathogen across an ecology to select against loss of the defense. This resistance switching strategy is evolutionarily stable, and provides a powerful evolutionary mechanism that maintains host-pathogen interactions and enables co-evolutionary dynamics in a wide range of systems.

scholarly journals Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

2015 ◽  
Vol 112 (21) ◽  
pp. 6676-6681 ◽  
Author(s):  
Adriaan van der Graaf ◽  
René Wardenaar ◽  
Drexel A. Neumann ◽  
Aaron Taudt ◽  
Ruth G. Shaw ◽  
...  
Keyword(s):  
Cytosine Methylation ◽  
Evolutionary Dynamics ◽  
Phenotypic Diversity ◽  
Natural Populations ◽  
Population Level ◽  
Genomic Context ◽  
Term Selection ◽  
Comprehensive Picture ◽  
Dynamic Interplay

Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences.

A Comparison of Threshold Strategies in Tomatoes and Soybean

2008 ◽  
Vol 22 (4) ◽  
pp. 729-735 ◽  
Author(s):  
Carlos D. Mayén ◽  
Kevin D. Gibson ◽  
Stephen C. Weller
Keyword(s):  
Weed Control ◽  
Seed Bank ◽  
Crop Yields ◽  
Control Strategies ◽  
Seed Banks ◽  
Weed Seed ◽  
Tomato Seed ◽  
Giant Foxtail ◽  
The Difference

Weed control strategies based on conserving crop yields rather than preventing weed seed production may result in increased weed densities and management costs over the long-term, particularly in less competitive crops such as tomatoes. The effect of crop, tillage, and duration of weed control on weed seed bank size and composition was examined from spring 2001 to spring 2003 near Lafayette, IN. Main plots in 2001 and 2002 contained soybean or tomato planted in rotation (soybean-tomato, tomato-soybean). Subplots were managed with either conventional or no-till practices. Sub-subplots contrasted threshold strategies in which weeds were either controlled for four to six weeks (period threshold, PT) or throughout the growing season (no-seed-threshold, NST). Seed banks were sampled annually in the spring. Emergent weeds were counted` at four and twelve weeks after planting (WAP) in 2001 and 2002. Weed seed banks did not significantly change in the NST plots in any year. However, seed bank densities increased substantially following tomatoes in PT plots. In contrast, weed seed bank densities decreased following soybeans in PT plots. The difference in seed banks and emergent weeds between soybean and tomatoes could be attributed primarily to greater suppression of giant foxtail by the soybean canopy. Giant foxtail control was greater in PT soybeans than in PT tomatoes in both years and giant foxtail comprised most of the PT tomato seed bank in 2002 and 2003. Tillage did not affect weed seed banks in any year. This study highlights the need to control later emerging weeds in tomatoes to prevent large increases in the weed seed bank.

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