Modelling evolution of genome size in prokaryotes in response to changes in their abiotic environment

The size of the genomes of known free-living prokaryotes varies from � 1:3 Mbp to � 13 Mbp. This thesis proposes a possible explanation of this variation due to variability of the physical conditions of the environment. In a stable environment, competition for the resource becomes the main force of selection and smaller (thus cheaper) genomes are favoured. In more variable conditions larger genomes will be preferred, as they have a wider range of response to a less predictable environment. An agent-based model (ABM) of genome evolution in an free-living prokaryotic population has been proposed. Using the classic Hutchinson niche space model, a gene was defined as a Gaussian function over a corresponding niche dimension. The cell can have more than one gene along a given dimension, and the envelope of all the corresponding responses is considered a full description of a cell’s phenotype over that dimension. Gene deletion, gene duplication, and modifying mutations are permitted during reproduction, so the number of genes and their phenotypic effect (height and position of the Gaussian envelope) are free to evolve. The surface under the curve is fixed to prevent ‘supergenes’ from occurring. Change of the environmental conditions is simulated as a bounded random walk with a varying length of the step (a parameter representing variability of the environment). Using this approach, the model is able to reproduce the phenomenon of genome streamlining in more stable environments (analogical to e.g. oligotrophic gyre regions of the ocean) and genome complexification in variable environments. Horizontal gene transfer (HGT) was also introduced, but was found to act in a similar manner as gene duplication and shown no important contribution to the speed of evolution and the adaptive potential of the population

A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments

Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand howorganisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results showthat a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt

The effect of extrinsic mortality on genome size evolution in prokaryotes

Mortality has a significant role in prokaryotic ecology and evolution, yet the impact of variations in extrinsic mortality on prokaryotic genome evolution has received little attention. We used both mathematical and agent-based models to reveal how variations in extrinsic mortality affect prokaryotic genome evolution. Our results suggest that the genome size of bacteria increases with increased mortality. A high extrinsic mortality increases the pool of free resources and shortens life expectancy, which selects for faster reproduction, a phenotype we called ‘scramblers’. This phenotype is realised by the expansion of gene families involved in nutrient acquisition and metabolism. In contrast, a low mortality rate increases an individual’s life expectancy, which results in natural selection favouring tolerance to starvation when conditions are unfavourable. This leads to the evolution of small, streamlined genomes (‘stayers’). Our models predict that large genomes, gene family expansion and horizontal gene transfer should be observed in prokaryotes occupying ecosystems exposed to high abiotic stress, as well as those under strong predator- and/or pathogen-mediated selection. A comparison of genome size of cyanobacteria in relatively stable marine versus more turbulent freshwater environments corroborates our predictions, although other factors between these environments could also be responsible

Evolution of major histocompatibility complex gene copy number.

MHC genes, which code for proteins responsible for presenting pathogen-derived antigens to the host immune system, show remarkable copy-number variation both between and within species. However, the evolutionary forces driving this variation are poorly understood. Here, we use computer simulations to investigate whether evolution of the number of MHC variants in the genome can be shaped by the number of pathogen species the host population encounters (pathogen richness). Our model assumed that while increasing a range of pathogens recognised, expressing additional MHC variants also incurs costs such as an increased risk of autoimmunity. We found that pathogen richness selected for high MHC copy number only when the costs were low. Furthermore, the shape of the association was modified by the rate of pathogen evolution, with faster pathogen mutation rates selecting for increased host MHC copy number, but only when pathogen richness was low to moderate. Thus, taking into account factors other than pathogen richness may help explain wide variation between vertebrate species in the number of MHC genes. Within population, variation in the number of unique MHC variants carried by individuals (INV) was observed under most parameter combinations, except at low pathogen richness. This variance gave rise to positive correlations between INV and host immunocompetence (proportion of pathogens recognised). However, within-population variation in host immunocompetence declined with pathogen richness. Thus, counterintuitively, pathogens can contribute more to genetic variance for host fitness in species exposed to fewer pathogen species, with consequences to predictions from "Hamilton-Zuk" theory of sexual selection

Evolution of physiological functions of melatonin in invertebrates

Melatonin is one of most widespread biological particles. Till now its presence is confirmed in vast range of organisms belonging to bacteria, protozoa, plants, fungi and animals. Recent studies show a large number of roles played by this small molecule. They vary from protective role in intracellular metabolism to involvement in photoperiodism and circadian behaviour and all this only among vertebrates. Those facts rise question about processes which lead to such diversity. We looked into the model of evolution of melatonin functions proposed by Hardeland and Poeggeler (2003). Authors suggest protective role in cell metabolism as free radical scavenger and antioxidant as the preliminary function of melatonin. Its relevance rose in cooperation with increasing concentration of oxygen both in cell and in environment (as a result of development of photosynthesis and mitochondria). As the photosynthesis is a circadian process concentration of oxygen in early atmosphere could also varied with circadian rhythm what could in turn cause rhythmic demand for antioxidant action. This process would later lead to endogenous circadian oscillation of melatonin concentration triggered by light what resulted in involvement in photoperiodically regulated actions. We confronted the proposed model with results of melatonin-linked studies held on invertebrates - a polyphyletic taxon which presents many types of organisms physiology and morphology. In some cases research teams found multilevel involvement of melatonin in biology of investigated species. On the contrary to vertebrates, invertebrates show not only day-peak pattern of melatonin circadian concentration. Also night peaks and lack of rhythm ware observed even in closely related species (e.g. Decapoda). Correlation between presence of exogenous melatonin and circadian behaviour modification was also shown in a few species. In spite of limited data and not large number of species investigated we can conclude that the model fits available data pretty well. Interesting conclusion of this review is that the new function of melatonin does not replace the older one, only develops in parallel. The natural selection process does not create a new attribute in response to environment challenge, it only adopts one of existing features of organisms

Anatomy of digital contact tracing: Role of age, transmission setting, adoption, and case detection

International audienc

Role of melatonin in the control of depth distribution of Daphnia magna

Previous studies confirmed the presence of melatonin in Daphnia magna and demonstrated diurnal fluctuations in its concentration. It is also known that in several invertebrate species, melatonin affects locomotor activity. We tested the hypothesis that this hormone is involved in the regulation of Daphnia diel vertical migration (DVM) behaviour that is well recognized as the adaptive response to predation threat. Using 'plankton organs', we studied the effect of three concentrations of exogenous melatonin (10-5, 10-7, 10-9 M) on DVM of both female and male D. magna in the presence or absence of chemical cue (kairomone) of planktivorous fish. Depth distribution was measured six times a day, using infrared-sensitive closed circuit television cameras. Our results showed a significant effect of melatonin on the mean depth of experimental populations, both males and females, but only when melatonin was combined with fish kairomone. Females stayed, on average, closer to the surface than males, both responding to the presence of kairomone by descending to deeper strata. In the presence of exogenous melatonin and with the threat of predation, Daphnia stayed closer to the surface and their distribution was more variable than that of individuals, which were exposed to the kairomone alone. Approaching the surface in the presence of predation threat seems to be maladaptive. We postulate the role of melatonin as a stress signal inhibitor in molecular pathways of response to predation threat in Cladocera