A simple stochastic model describing genomic evolution over time of GC content in microbial symbionts

Bohlin, Jon; Rose, Brittany; Brynildsrud, Ola Brønstad; Blasio, Birgitte Freiesleben de

doi:10.1016/j.jtbi.2020.110389

Cited by 8 publications

(33 citation statements)

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“…In particular, the present work is an extension of a model describing the evolution of genomic GC content as a consequence of AT/GC mutation rates with random perturbations for microbial symbionts [9]. As there are many similarities between present-and the previous work on microbial symbionts [9] only the steps separating these models and details necessary for a complete comprehension are included.…”

Section: The Mathematical Modelmentioning

confidence: 99%

“…For larger multi-cellular organisms the GC content is fairly stable between species although there can be local genomic differences, for instance CpG islands which are usually not present in prokaryotes [8]. For prokaryotes within-species genomic GC content is stable while GC content between different species can vary substantially, from 13.5% GC to 75% GC [9]. This variation in genomic GC content appears to have both an environmental component as well as a phylogenetic one [15,36].…”

Section: Introductionmentioning

confidence: 99%

“…A previous study [9] modelling the evolution of GC content in microbes living in a stable symbiotic relationship with an eukaryotic host, usually insects, suggested that AT → GC mutation rates, and vice versa, may determine the symbiotic species fate early on in the organism's history providing mutation rates are approximately constant. Microbial symbionts often live in low density populations, are unable to perform homologous recombination and lack many DNA repair genes implying that mutations accumulate, often in a clock-like manner [29].…”

Section: Introductionmentioning

confidence: 99%

“…Since microbial symbionts live in a stable environment with their eukaryotic host it makes sense to model the random perturbations of their AT-and GC mutation rates as a Gaussian white noise multiplied by a constant, or a fixed parameter, to be estimated, as has previously been done [9]. For asexually reproducing organisms in general, subjected to differing selective pressures over time, it is more natural to model random perturbations of AT/GC mutation rates as a Gaussian white noise multiplied by a function varying with respect to time.…”

Section: Introductionmentioning

confidence: 99%

“…For asexually reproducing organisms in general, subjected to differing selective pressures over time, it is more natural to model random perturbations of AT/GC mutation rates as a Gaussian white noise multiplied by a function varying with respect to time. As such, the purpose of the present work is to expand on the previous study [9]. That is, to model the evolution of genomic GC content as a consequence of AT → GC, as well as GC → AT, mutation rates subject to random perturbations c(t) over time t, as opposed to a constant c, for all non-recombining, Chargaff parity law compliant organisms, regardless of which kingdom they belong to.…”

Section: Introductionmentioning

confidence: 99%

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A simple model describing evolution of genomic GC content with random perturbations in asexually reproducing organisms

Bohlin¹

2022

Preprint

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Section: The Mathematical Modelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A simple model describing evolution of genomic GC content with random perturbations in asexually reproducing organisms

Bohlin¹

2022

Preprint

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A simple stochastic model describing the evolution of genomic GC content in asexually reproducing organisms

Bohlin

2022

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A genome’s nucleotide composition can usually be summarized with (G)uanine + (C)ytosine (GC) or (A)denine + (T)hymine (AT) frequencies as GC% = 100% − AT%. Genomic AT/GC content has been linked to environment and selective processes in asexually reproducing organisms. A model is presented relating the evolution of genomic GC content over time to AT $$\rightarrow$$ → GC and GC $$\rightarrow$$ → AT mutation rates. By employing Itô calculus it is shown that if mutation rates are subject to random perturbations, that can vary over time, several implications follow. In particular, an extra Brownian motion term appears influencing genomic nucleotide variability; the greater the random perturbations the more genomic nucleotide variability. This can have several interpretations depending on the context. For instance, reducing the influence of the random perturbations on the AT/GC mutation rates and thus genomic nucleotide variability, to limit fitness decreasing and deleterious mutations, will likely suggest channeling of resources. On the other hand, increased genomic nucleotide diversity may be beneficial in variable environments. In asexually reproducing organisms, the Brownian motion term can be considered to be inversely reflective of the selective pressures an organism is subjected to at the molecular level. The presented model is a generalization of a previous model, limited to microbial symbionts, to all asexually reproducing, non-recombining organisms. Last, a connection between the presented model and the classical Luria–Delbrück mutation model is presented in an Itô calculus setting.

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Human Follicular Mites: Ectoparasites Becoming Symbionts

Smith

Manzano-Marı́n

Reyes-Prieto

et al. 2022

Molecular Biology and Evolution

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Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans tha continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic or endosymbiotic lifestyle. Somatic nuclei show underreplication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

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A simple stochastic model describing genomic evolution over time of GC content in microbial symbionts

Cited by 8 publications

References 42 publications

A simple model describing evolution of genomic GC content with random perturbations in asexually reproducing organisms

A simple model describing evolution of genomic GC content with random perturbations in asexually reproducing organisms

A simple stochastic model describing the evolution of genomic GC content in asexually reproducing organisms

Human Follicular Mites: Ectoparasites Becoming Symbionts

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