Molecular Evolutionary Dynamics of Energy Limited Microorganisms

Shoemaker, William R.; Polezhaeva, Evgeniya; Givens, Kenzie B.; Lennon, Jay T.

doi:10.1093/molbev/msab195

Cited by 7 publications

(20 citation statements)

References 63 publications

(85 reference statements)

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“…Similar to a previous analysis [31], it is likely that gene identity was again too coarse a measure to determine whether convergent or divergent evolution occurred. While ∆spo0A is a master regulatory gene, its removal may only have slightly perturbed the rates of evolution for a large number of genes in a given environment.…”

Section: Parallelism and (Con/di)vergence At The Gene Levelmentioning

confidence: 67%

“…S5,6), suggesting that, generally, the direction of evolution at the gene-level tended towards convergence rather than divergence. We found that this is the case, as the degree of overlap in enriched genes relative to a null distribution [31] suggests convergent evolution (Fig. S9).…”

Section: Parallelism and (Con/di)vergence At The Gene Levelmentioning

confidence: 76%

“…Populations were regularly plated to test for contamination. An identical experiment was concurrently run with the WT strain, which was previously described [31].…”

Section: Transfer Protocol Sequencing and Variant Callingmentioning

confidence: 99%

“…However, an unknown number of generations likely occurred while populations remained in stationary phase due to cells using dead cells as a nutrient source. This "cryptic growth" [25,[31][32][33] suggests that the estimated number of generations likely represents the true number of generations for 1-day transfers, while it is closer to an estimate of the minimum number of generations for 10 and 100-day transfers.…”

Section: Transfer Protocol Sequencing and Variant Callingmentioning

confidence: 99%

“…We tested for divergent/convergent evolution by examining the overlap of I between WT and ∆spo0A populations and populations from all three transfer regimes and comparing them to a null hypergeometric distribution as previously described [31]. To examine convergent/divergent evolution among enriched genes, we calculated the vector of relative multiplicities (M i = m i / m i ) and compared the mean absolute difference between I genes for a given pair of transfer regimes or genetic backgrounds as…”

Section: Parallelism At the Gene Levelmentioning

confidence: 99%

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Seed banks alter the molecular evolutionary dynamics ofBacillus subtilis

Shoemaker

Polezhaeva

Givens

et al. 2021

Preprint

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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.

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Section: Parallelism and (Con/di)vergence At The Gene Levelmentioning

confidence: 67%

Section: Parallelism and (Con/di)vergence At The Gene Levelmentioning

confidence: 76%

“…Populations were regularly plated to test for contamination. An identical experiment was concurrently run with the WT strain, which was previously described [31].…”

Section: Transfer Protocol Sequencing and Variant Callingmentioning

confidence: 99%

Section: Transfer Protocol Sequencing and Variant Callingmentioning

confidence: 99%

Section: Parallelism At the Gene Levelmentioning

confidence: 99%

See 3 more Smart Citations

Seed banks alter the molecular evolutionary dynamics ofBacillus subtilis

Shoemaker

Polezhaeva

Givens

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

Seed banks alter the molecular evolutionary dynamics ofBacillus subtilis

et al. 2022

Self Cite

View full text Add to dashboard Cite

Fluctuations in the availability of resources constrains the growth and reproduction of individuals, which subsequently effects the evolution of their respective populations. Many organisms contend with such 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. The ability of these bacteria to enter a dormant state increased the accumulation of genetic diversity over time and altered the trajectory of mutations, findings that were recapitulated using simulations based on a mathematical model of evolutionary dynamics. While the ability to form a seed bank did not alter the degree of negative selection, we found that it consistently altered the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank can affect the direction and rate of molecular evolution over an extended evolutionary timescale.

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Genomic stasis over millions of years in subseafloor sediment

Garber,

Ramírez,

D'Hondt

2024

Environmental Microbiology

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One of the significant challenges in microbiology is to understand the extent and mechanisms of evolution within life beneath the surface of the Earth. The population bottleneck that microbes in deep marine sediment experience implies that mutational and population genetic forces could lead to higher levels of relaxed selection and an increase in pseudogenes. To investigate this hypothesis, a group of Thalassospira strains were isolated from subseafloor sediment that is 3 to 6 million years old, as reported by Orsi and colleagues in 2021. These isolates, representing lineages that have been buried for millions of years, offer an excellent opportunity to study the evolution of life beneath the seafloor over a long period. The existence of closely related strains from environments on the surface of the Earth enabled us to examine the impact of selection within each group. We discovered that isolates from beneath the seafloor show lineage‐specific similarities to Thalassospira from the surface world, both in the overall intensity of selection on the genome and in the specific genes affected by mutation. We found no signs of increased relaxed selection or other notable genomic changes in the genomes of the Thalassospira isolates from beneath the seafloor, suggesting that these subseafloor isolates were awakened from a million‐year near‐stasis. The unique genomic characteristics of each Thalassospira lineage from beneath the seafloor must then reflect genetic changes that surface‐inhabiting decendants acquired in the past 3–6 million years. Remarkably, Thalassospira lineages beneath the surface appear to have stably maintained their genomes in the midst of metabolic dormancy and extremely long generation times.

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Molecular Evolutionary Dynamics of Energy Limited Microorganisms

Cited by 7 publications

References 63 publications

Seed banks alter the molecular evolutionary dynamics ofBacillus subtilis

Seed banks alter the molecular evolutionary dynamics ofBacillus subtilis

Seed banks alter the molecular evolutionary dynamics ofBacillus subtilis

Genomic stasis over millions of years in subseafloor sediment

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