scholarly journals Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

2021 ◽  
Author(s):  
Gabrielle L. Harrow ◽  
John A. Lees ◽  
William P. Hanage ◽  
Marc Lipsitch ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Bacterial Population ◽  
Genomic Data ◽  
Genetic Distances ◽  
Outbreeding Depression ◽  
Short Term ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Population Structures ◽  
Negative Frequency Dependent Selection

AbstractStreptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations’ ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.

scholarly journals Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures

2020 ◽  
Author(s):  
Gabrielle L. Harrow ◽  
John A. Lees ◽  
William P. Hanage ◽  
Marc Lipsitch ◽  
Jukka Corander ◽  
...  
Keyword(s):  
Bacterial Population ◽  
Genomic Data ◽  
Genetic Distances ◽  
Short Term ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Neutral Drift ◽  
Population Structures ◽  
Negative Frequency Dependent Selection ◽  
Multiple Strains

AbstractStreptococcus pneumoniae can be split into multiple strains, each with a characteristic combination of core and accessory genome variation, able to co-circulate and compete within the same hosts. Previous analyses of epidemiological datasets suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), acting to maintain accessory loci at equilibrium frequencies. To test whether this model could explain how such multi-strain populations were generated, it was modified to incorporate recombination. The outputs of simulations featuring symmetrical recombination were compared with genomic data on locus frequencies and distributions between genotypes, pairwise genetic distances and tree shape. These demonstrated NFDS prevented the loss of variation through neutral drift, but generated unstructured populations of diverse isolates. Making recombination asymmetrical, favouring deletion of accessory loci over insertion, alongside multi-locus NFDS significantly improved the fit to genomic data. In a population at equilibrium, structuring into multiple strains was stable due to outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. As many bacteria inhibit the integration of insertions into their chromosomes, this combination of asymmetrical recombination and multi-locus NFDS may underlie the co-existence of strains within a single ecological niche.

scholarly journals A geographic cline induced by negative frequency-dependent selection

2011 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuma Takahashi ◽  
Satoru Morita ◽  
Jin Yoshimura ◽  
Mamoru Watanabe
Keyword(s):  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Negative Frequency Dependent Selection

scholarly journals Intruder colour and light environment jointly determine how nesting male stickleback respond to simulated territorial intrusions

2016 ◽  
Vol 12 (8) ◽  
pp. 20160467 ◽  
Author(s):  
Daniel I. Bolnick ◽  
Kimberly Hendrix ◽  
Lyndon Alexander Jordan ◽  
Thor Veen ◽  
Chad D. Brock
Keyword(s):  
Frequency Dependence ◽  
Three Dimensional ◽  
Light Environment ◽  
Depth Gradient ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Negative Frequency Dependent Selection ◽  
Colour Signals

Variation in male nuptial colour signals might be maintained by negative frequency-dependent selection. This can occur if males are more aggressive towards rivals with locally common colour phenotypes. To test this hypothesis, we introduced red or melanic three-dimensional printed-model males into the territories of nesting male stickleback from two optically distinct lakes with different coloured residents. Red-throated models were attacked more in the population with red males, while melanic models were attacked more in the melanic male lake. Aggression against red versus melanic models also varied across a depth gradient within each lake, implying that the local light environment also modulated the strength of negative frequency dependence acting on male nuptial colour.

scholarly journals Negative frequency-dependent selection maintains coexisting genotypes during fluctuating selection

2019 ◽  
Author(s):  
Caroline B. Turner ◽  
Sean W. Buskirk ◽  
Katrina B. Harris ◽  
Vaughn S. Cooper
Keyword(s):  
Evolutionary Dynamics ◽  
Burkholderia Cenocepacia ◽  
Natural Environments ◽  
Fluctuating Selection ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Fluctuating Environment ◽  
Fluctuating Environments ◽  
Negative Frequency Dependent Selection ◽  
Selection For

AbstractNatural environments are rarely static; rather selection can fluctuate on time scales ranging from hours to centuries. However, it is unclear how adaptation to fluctuating environments differs from adaptation to constant environments at the genetic level. For bacteria, one key axis of environmental variation is selection for planktonic or biofilm modes of growth. We conducted an evolution experiment with Burkholderia cenocepacia, comparing the evolutionary dynamics of populations evolving under constant selection for either biofilm formation or planktonic growth with populations in which selection fluctuated between the two environments on a weekly basis. Populations evolved in the fluctuating environment shared many of the same genetic targets of selection as those evolved in constant biofilm selection, but were genetically distinct from the constant planktonic populations. In the fluctuating environment, mutations in the biofilm-regulating genes wspA and rpfR rose to high frequency in all replicate populations. A mutation in wspA first rose rapidly and nearly fixed during the initial biofilm phase but was subsequently displaced by a collection of rpfR mutants upon the shift to the planktonic phase. The wspA and rpfR genotypes coexisted via negative frequency-dependent selection around an equilibrium frequency that shifted between the environments. The maintenance of coexisting genotypes in the fluctuating environment was unexpected. Under temporally fluctuating environments coexistence of two genotypes is only predicted under a narrow range of conditions, but the frequency-dependent interactions we observed provide a mechanism that can increase the likelihood of coexistence in fluctuating environments.

scholarly journals Negative frequency dependent selection contributes to the maintenance of a global polymorphism in mitochondrial DNA

2020 ◽  
Vol 20 (1) ◽  
Author(s):  
Zorana Kurbalija Novičić ◽  
Ahmed Sayadi ◽  
Mihailo Jelić ◽  
Göran Arnqvist
Keyword(s):  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Life History ◽  
Balancing Selection ◽  
Food Resource ◽  
Ecological Processes ◽  
Central Process ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Negative Frequency Dependent Selection

Abstract Background Understanding the forces that maintain diversity across a range of scales is at the very heart of biology. Frequency-dependent processes are generally recognized as the most central process for the maintenance of ecological diversity. The same is, however, not generally true for genetic diversity. Negative frequency dependent selection, where rare genotypes have an advantage, is often regarded as a relatively weak force in maintaining genetic variation in life history traits because recombination disassociates alleles across many genes. Yet, many regions of the genome show low rates of recombination and genetic variation in such regions (i.e., supergenes) may in theory be upheld by frequency dependent selection. Results We studied what is essentially a ubiquitous life history supergene (i.e., mitochondrial DNA) in the fruit fly Drosophila subobscura, showing sympatric polymorphism with two main mtDNA genotypes co-occurring in populations world-wide. Using an experimental evolution approach involving manipulations of genotype starting frequencies, we show that negative frequency dependent selection indeed acts to maintain genetic variation in this region. Moreover, the strength of selection was affected by food resource conditions. Conclusions Our work provides novel experimental support for the view that balancing selection through negative frequency dependency acts to maintain genetic variation in life history genes. We suggest that the emergence of negative frequency dependent selection on mtDNA is symptomatic of the fundamental link between ecological processes related to resource use and the maintenance of genetic variation.

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