scholarly journals Population density affects the outcome of competition in co-cultures of Gardnerella species isolated from the human vaginal microbiome

2021 ◽  
Author(s):  
Salahuddin Khan ◽  
Janet E. Hill
Keyword(s):  
Population Density ◽  
Rare Species ◽  
Initial Density ◽  
Dynamic Environment ◽  
Amplicon Sequencing ◽  
Selective Advantage ◽  
Vaginal Microbiome ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Negative Frequency Dependent Selection

AbstractNegative frequency-dependent selection is one possible mechanism for maintenance of rare species in communities, but the selective advantage of rare species may be checked at lower overall population densities where resources are abundant. Gardnerella spp. belonging to cpn60 subgroup D, are detected at low levels in vaginal microbiomes and are nutritional generalists relative to other more abundant Gardnerella spp., making them good candidates for negative frequency-dependent selection. The vaginal microbiome is a dynamic environment and the resulting changes in density of the microbiota may explain why subgroup D never gains dominance. To test this, we co-cultured subgroup D isolates with isolates from the more common and abundant subgroup C. Deep amplicon sequencing of rpoB was used to determine proportional abundance of each isolate at 0 h and 72 h in 152 co-cultures, and to calculate change in proportion. D isolates had a positive change in proportional abundance in most co-cultures regardless of initial proportion. Initial density affected the change in proportion of subgroup D isolates either positively or negatively depending on the particular isolates combined, suggesting that growth rate, population density and other intrinsic features of the isolates influenced the outcome. Our results demonstrate that population density is an important factor influencing the outcome of competition between Gardnerella spp. isolated from the human vaginal microbiome.

scholarly journals A generalist lifestyle allows rare Gardnerella spp. to persist at low levels in the vaginal microbiome

2020 ◽  
Author(s):  
Salahuddin Khan ◽  
Sarah J. Vancuren ◽  
Janet E. Hill
Keyword(s):  
Growth Rate ◽  
Amino Acid ◽  
Carbon Sources ◽  
Niche Overlap ◽  
The Other ◽  
Acid Uptake ◽  
Vaginal Microbiome ◽  
Frequency Dependent ◽  
Frequency Dependent Selection ◽  
Negative Frequency Dependent Selection

AbstractGardnerella spp. are considered a hallmark of bacterial vaginosis, a dysbiosis of the vaginal microbiome. There are four cpn60 sequence-based subgroups within the genus (A, B, C, and D), and thirteen genome species have been defined recently. Gardnerella spp. co-occur in the vaginal microbiome with varying abundance, and these patterns are shaped by a resource-dependent, exploitative competition, which affects the growth rate of subgroup A, B, and C negatively. The growth rate of rarely abundant subgroup D, however, increases with the increasing number of competitors, negatively affecting the growth rate of others. We hypothesized that a nutritional generalist lifestyle and minimal niche overlap with the other, more abundant Gardnerella spp. facilitate the maintenance of subgroup D in the vaginal microbiome through negative-frequency dependent selection. Using 40 whole genome sequences from isolates representing all four subgroups we found that they could be distinguished based on content of their predicted proteomes. Proteins associated with carbohydrate and amino acid uptake and metabolism were significant contributors to the separation of subgroups. Subgroup D isolates had significantly more of their proteins assigned to amino acid metabolism than the other subgroups. Subgroup D isolates were also significantly different from others in terms of number and type of carbon sources utilized in a phenotypic assay, while the other three could not be distinguished. Overall, the results suggest that a generalist lifestyle and lack of niche overlap with other Gardnerella spp. leads to subgroup D being favoured by negative-frequency dependent selection in the vaginal microbiome.

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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