scholarly journals Rapid selective sweep of pre-existing polymorphisms and slow fixation of new mutations in experimental evolution of Desulfovibrio vulgaris

2015 ◽  
Vol 9 (11) ◽  
pp. 2360-2372 ◽  
Author(s):  
Aifen Zhou ◽  
Kristina L Hillesland ◽  
Zhili He ◽  
Wendy Schackwitz ◽  
Qichao Tu ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Selective Sweep ◽  
Desulfovibrio Vulgaris ◽  
New Mutations

scholarly journals Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

2020 ◽  
Vol 14 (11) ◽  
pp. 2862-2876
Author(s):  
Bo Wu ◽  
Feifei Liu ◽  
Aifen Zhou ◽  
Juan Li ◽  
Longfei Shu ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Nitrate Tolerance ◽  
Desulfovibrio Vulgaris ◽  
Tolerance Mechanisms

scholarly journals Distinct Patterns of Selective Sweep and Polygenic Adaptation in Evolve and Resequence Studies

2020 ◽  
Vol 12 (6) ◽  
pp. 890-904 ◽  
Author(s):  
Neda Barghi ◽  
Christian Schlötterer
Keyword(s):  
Experimental Evolution ◽  
Selective Sweep ◽  
Time Series Data ◽  
Empirical Studies ◽  
Series Data ◽  
Stabilizing Selection ◽  
Selection Signatures ◽  
Polygenic Adaptation ◽  
Frequency Changes ◽  
Optimum Model

Abstract In molecular population genetics, adaptation is typically thought to occur via selective sweeps, where targets of selection have independent effects on the phenotype and rise to fixation, whereas in quantitative genetics, many loci contribute to the phenotype and subtle frequency changes occur at many loci during polygenic adaptation. The sweep model makes specific predictions about frequency changes of beneficial alleles and many test statistics have been developed to detect such selection signatures. Despite polygenic adaptation is probably the prevalent mode of adaptation, because of the traditional focus on the phenotype, we are lacking a solid understanding of the similarities and differences of selection signatures under the two models. Recent theoretical and empirical studies have shown that both selective sweep and polygenic adaptation models could result in a sweep-like genomic signature; therefore, additional criteria are needed to distinguish the two models. With replicated populations and time series data, experimental evolution studies have the potential to identify the underlying model of adaptation. Using the framework of experimental evolution, we performed computer simulations to study the pattern of selected alleles for two models: 1) adaptation of a trait via independent beneficial mutations that are conditioned for fixation, that is, selective sweep model and 2) trait optimum model (polygenic adaptation), that is adaptation of a quantitative trait under stabilizing selection after a sudden shift in trait optimum. We identify several distinct patterns of selective sweep and trait optimum models in populations of different sizes. These features could provide the foundation for development of quantitative approaches to differentiate the two models.

scholarly journals Effects of Genetic and Physiological Divergence on the Evolution of a Sulfate-Reducing Bacterium under Conditions of Elevated Temperature

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Megan L. Kempher ◽  
Xuanyu Tao ◽  
Rong Song ◽  
Bo Wu ◽  
David A. Stahl ◽  
...  
Keyword(s):  
Natural Selection ◽  
Elevated Temperature ◽  
Experimental Evolution ◽  
Evolutionary Biology ◽  
Desulfovibrio Vulgaris ◽  
Common Environment ◽  
Content Type ◽  
Sulfate Reducing ◽  
Evolution Study ◽  
The Impact

ABSTRACT Adaptation via natural selection is an important driver of evolution, and repeatable adaptations of replicate populations, under conditions of a constant environment, have been extensively reported. However, isolated groups of populations in nature tend to harbor both genetic and physiological divergence due to multiple selective pressures that they have encountered. How this divergence affects adaptation of these populations to a new common environment remains unclear. To determine the impact of prior genetic and physiological divergence in shaping adaptive evolution to accommodate a new common environment, an experimental evolution study with the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough (DvH) was conducted. Two groups of replicate populations with genetic and physiological divergence, derived from a previous evolution study, were propagated in an elevated-temperature environment for 1,000 generations. Ancestor populations without prior experimental evolution were also propagated in the same environment as a control. After 1,000 generations, all the populations had increased growth rates and all but one had greater fitness in the new environment than the ancestor population. Moreover, improvements in growth rate were moderately affected by the divergence in the starting populations, while changes in fitness were not significantly affected. The mutations acquired at the gene level in each group of populations were quite different, indicating that the observed phenotypic changes were achieved by evolutionary responses that differed between the groups. Overall, our work demonstrated that the initial differences in fitness between the starting populations were eliminated by adaptation and that phenotypic convergence was achieved by acquisition of mutations in different genes. IMPORTANCE Improving our understanding of how previous adaptation influences evolution has been a long-standing goal in evolutionary biology. Natural selection tends to drive populations to find similar adaptive solutions for the same selective conditions. However, variations in historical environments can lead to both physiological and genetic divergence that can make evolution unpredictable. Here, we assessed the influence of divergence on the evolution of a model sulfate-reducing bacterium, Desulfovibrio vulgaris Hildenborough, in response to elevated temperature and found a significant effect at the genetic but not the phenotypic level. Understanding how these influences drive evolution will allow us to better predict how bacteria will adapt to various ecological constraints.

scholarly journals Adaptation in isolated populations: when does it happen and when can we tell?

2016 ◽  
Author(s):  
Jessica L. Crisci ◽  
Matthew D. Dean ◽  
Peter Ralph
Keyword(s):  
Positive Selection ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Selective Sweep ◽  
Small Population ◽  
Optimal Combination ◽  
Isolated Populations ◽  
Standing Variation ◽  
Exciting Opportunity ◽  
Subsequent Selection

AbstractIsolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans for positive selection in such populations have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affects the ability of outlier scans for selection to identify adaptive alleles using both single site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur, and yet the adaptive variants are most likely to derive from a single ancestor (a “hard” selective sweep); in this zone, four commonly used statistics detect selection with high power. Real-world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole genome sequencing of differentiated populations.

scholarly journals Characterization of NaCl tolerance in Desulfovibrio vulgaris Hildenborough through experimental evolution

2013 ◽  
Vol 7 (9) ◽  
pp. 1790-1802 ◽  
Author(s):  
Aifen Zhou ◽  
Edward Baidoo ◽  
Zhili He ◽  
Aindrila Mukhopadhyay ◽  
Jason K Baumohl ◽  
...  
Keyword(s):  
Experimental Evolution ◽  
Desulfovibrio Vulgaris ◽  
Nacl Tolerance ◽  
Desulfovibrio Vulgaris Hildenborough

scholarly journals Genetic Adaptation to Salt Stress in Experimental Evolution of Desulfovibrio vulgaris Hildenborough

2010 ◽  
Author(s):  
Aifen Zhou ◽  
Kristina Hillesland ◽  
Zhili He ◽  
Marcin Joachimiak ◽  
Grant Zane ◽  
...  
Keyword(s):  
Salt Stress ◽  
Experimental Evolution ◽  
Desulfovibrio Vulgaris ◽  
Genetic Adaptation ◽  
Desulfovibrio Vulgaris Hildenborough

Hitchhiking and Selective Sweeps

2018 ◽  
Author(s):  
Bruce Walsh ◽  
Michael Lynch
Keyword(s):  
Codon Bias ◽  
Common Ancestor ◽  
Selective Sweep ◽  
Favorable Allele ◽  
Effective Population ◽  
Different Types ◽  
History Of ◽  
Genomic Regions ◽  
Considerable Body ◽  
New Mutations

When a favorable allele increases in frequency, it alters the coalescent structure (the pattern of times back to a common ancestor) at linked sites relative to that under drift. This creates patterns of sequence polymorphism than can be used to potentially detect ongoing, or very recent, selection. This idea of a neutral allele hitchhiking up to high frequency when coupled to a favorable allele is the notion of a selective sweep, and this chapter reviews the considerable body of associated population-genetics theory on sweeps. Different types of sweeps leave different signatures, resulting in the very diverse collection of tests of selection discussed in Chapter 9. Either a history of recurrent sweeps, or of background selection, results in linked genomic regions of reduced effective population size. This implies that more mutations in sich regions are efficiently neutral, which can result in increased substitution rates and lower codon bias. Finally, the chapter examines the theory for when response is expected to start from existing variation, as opposed to waiting for the appearance of new mutations.

scholarly journals Genetic Basis of Chromate Adaptation and the Role of the Pre-existing Genetic Divergence during an Experimental Evolution Study with Desulfovibrio vulgaris Populations

mSystems ◽  
2021 ◽  
Author(s):  
Weiling Shi ◽  
Qiao Ma ◽  
Feiyan Pan ◽  
Yupeng Fan ◽  
Megan L. Kempher ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Experimental Evolution ◽  
Genetic Basis ◽  
Functional Genes ◽  
Desulfovibrio Vulgaris ◽  
Content Type ◽  
Metal Pollutants ◽  
Evolution Study ◽  
Heavy Metal Pollutants

Chromium is one of the most common heavy metal pollutants of soil and groundwater. The potential of Desulfovibrio vulgaris Hildenborough in heavy metal bioremediation such as Cr(VI) reduction was reported previously; however, experimental evidence of key functional genes involved in Cr(VI) resistance are largely unknown.

scholarly journals Key Metabolites and Mechanistic Changes for Salt Tolerance in an Experimentally Evolved Sulfate-Reducing Bacterium, Desulfovibrio vulgaris

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Aifen Zhou ◽  
Rebecca Lau ◽  
Richard Baran ◽  
Jincai Ma ◽  
Frederick von Netzer ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Experimental Evolution ◽  
High Salinity ◽  
Desulfovibrio Vulgaris ◽  
Salt Adaptation ◽  
Toxic Heavy Metals ◽  
Natural Habitats ◽  
Adaptation Mechanism ◽  
Sulfate Reducing

ABSTRACT Rapid genetic and phenotypic adaptation of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough to salt stress was observed during experimental evolution. In order to identify key metabolites important for salt tolerance, a clone, ES10-5, which was isolated from population ES10 and allowed to experimentally evolve under salt stress for 5,000 generations, was analyzed and compared to clone ES9-11, which was isolated from population ES9 and had evolved under the same conditions for 1,200 generations. These two clones were chosen because they represented the best-adapted clones among six independently evolved populations. ES10-5 acquired new mutations in genes potentially involved in salt tolerance, in addition to the preexisting mutations and different mutations in the same genes as in ES9-11. Most basal abundance changes of metabolites and phospholipid fatty acids (PLFAs) were lower in ES10-5 than ES9-11, but an increase of glutamate and branched PLFA i17:1ω9c under high-salinity conditions was persistent. ES9-11 had decreased cell motility compared to the ancestor; in contrast, ES10-5 showed higher cell motility under both nonstress and high-salinity conditions. Both genotypes displayed better growth energy efficiencies than the ancestor under nonstress or high-salinity conditions. Consistently, ES10-5 did not display most of the basal transcriptional changes observed in ES9-11, but it showed increased expression of genes involved in glutamate biosynthesis, cation efflux, and energy metabolism under high salinity. These results demonstrated the role of glutamate as a key osmolyte and i17:1ω9c as the major PLFA for salt tolerance in D. vulgaris. The mechanistic changes in evolved genotypes suggested that growth energy efficiency might be a key factor for selection. IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution. IMPORTANCE High salinity (e.g., elevated NaCl) is a stressor that affects many organisms. Salt tolerance, a complex trait involving multiple cellular pathways, is attractive for experimental evolutionary studies. Desulfovibrio vulgaris Hildenborough is a model sulfate-reducing bacterium (SRB) that is important in biogeochemical cycling of sulfur, carbon, and nitrogen, potentially for bio-corrosion, and for bioremediation of toxic heavy metals and radionuclides. The coexistence of SRB and high salinity in natural habitats and heavy metal-contaminated field sites laid the foundation for the study of salt adaptation of D. vulgaris Hildenborough with experimental evolution. Here, we analyzed a clone that evolved under salt stress for 5,000 generations and compared it to a clone evolved under the same condition for 1,200 generations. The results indicated the key roles of glutamate for osmoprotection and of i17:1ω9c for increasing membrane fluidity during salt adaptation. The findings provide valuable insights about the salt adaptation mechanism changes during long-term experimental evolution.

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