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Register a new userNon-genetic variability: survival strategy or nuisance?
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The observation that phenotypic variability is ubiquitous in isogenic populations has led to a multitude of experimental and theoretical studies seeking to probe the causes and consequences of this variability. Whether it be in the context of antibiotic treatments or exponential growth in constant environments, non-genetic variability has shown to have significant effects on population dynamics. Here, we review research that elucidates the relationship between cell-to-cell variability and population dynamics. After summarizing the relevant experimental observations, we discuss models of bet-hedging and phenotypic switching. In the context of these models, we discuss how switching between phenotypes at the single-cell level can help populations survive in uncertain environments. Next, we review more fine-grained models of phenotypic variability where the relationship between single-cell growth rates, generation times and cell sizes is explicitly considered. Variability in these traits can have significant effects on the population dynamics, even in a constant environment. We show how these effects can be highly sensitive to the underlying model assumptions. We close by discussing a number of open questions, such as how environmental and intrinsic variability interact and what the role of non-genetic variability in evolutionary dynamics is.
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Biological systems are typically highly open, non-equilibrium systems that are very challenging to understand from a statistical mechanics perspective. While statistical treatments of evolutionary biological systems have a long and rich history, examination of the time-dependent non-equilibrium dynamics has been less studied. In this paper we first derive a generalized master equation in the genotype space for diploid organisms incorporating the processes of selection, mutation, recombination, and reproduction. The master equation is defined in terms of continuous time and can handle an arbitrary number of gene loci and alleles, and can be defined in terms of an absolute population or probabilities. We examine and analytically solve several prototypical cases which illustrate the interplay of the various processes and discuss the timescales of their evolution. The entropy production during the evolution towards steady state is calculated and we find that it agrees with predictions from non-equilibrium statistical mechanics where it is large when the population distribution evolves towards a more viable genotype. The stability of the non-equilibrium steady state is confirmed using the Glansdorff-Prigogine criterion.
A crop can be represented as a biotechnical system in which components are either chosen (cultivar, management) or given (soil, climate) and whose combination generates highly variable stress patterns and yield responses. Here, we used modeling and simulation to predict the crop phenotypic plasticity resulting from the interaction of plant traits (G), climatic variability (E) and management actions (M). We designed two in silico experiments that compared existing and virtual sunflower cultivars (Helianthus annuus L.) in a target population of cropping environments by simulating a range of indicators of crop performance. Optimization methods were then used to search for GEM combinations that matched desired crop specifications. Computational experiments showed that the fit of particular cultivars in specific environments is gradually increasing with the knowledge of pedo-climatic conditions. At the regional scale, tuning the choice of cultivar impacted crop performance the same magnitude as the effect of yearly genetic progress made by breeding. When considering virtual genetic material, designed by recombining plant traits, cultivar choice had a greater positive impact on crop performance and stability. Results suggested that breeding for key traits conferring plant plasticity improved cultivar global adaptation capacity whereas increasing genetic diversity allowed to choose cultivars with distinctive traits that were more adapted to specific conditions. Consequently, breeding genetic material that is both plastic and diverse may improve yield stability of agricultural systems exposed to climatic variability. We argue that process-based modeling could help enhancing spatial management of cultivated genetic diversity and could be integrated in functional breeding approaches.
We propose a method that uses genetic data to test for the occurrence of a recent range expansion and to infer the location of the origin of the expansion. We introduce a statistic for pairs of populations $psi$ (the directionality index) that detects asymmetries in the two-dimensional allele frequency spectrum caused by the series of founder events that happen during an expansion. Such asymmetry arises because low frequency alleles tend to be lost during founder events, thus creating clines in the frequencies of surviving low-frequency alleles. Using simulations, we further show that $psi$ is more powerful for detecting range expansions than both $F_{ST}$ and clines in heterozygosity. We illustrate the utility of $psi$ by applying it to a data set from modern humans and show how we can include more complicated scenarios such as multiple expansion origins or barriers to migration in the model.
Range expansion and range shifts are crucial population responses to climate change. Genetic consequences are not well understood but are clearly coupled to ecological dynamics that, in turn, are driven by shifting climate conditions. We model a population with a deterministic reaction-- diffusion model coupled to a heterogeneous environment that develops in time due to climate change. We decompose the resulting travelling wave solution into neutral genetic components to analyse the spatio-temporal dynamics of its genetic structure. Our analysis shows that range expansions and range shifts under slow climate change preserve genetic diversity. This is because slow climate change creates range boundaries that promote spatial mixing of genetic components. Mathematically , the mixing leads to so-called pushed travelling wave solutions. This mixing phenomenon is not seen in spatially homogeneous environments, where range expansion reduces genetic diversity through gene surfing arising from pulled travelling wave solutions. However, the preservation of diversity is diminished when climate change occurs too quickly. Using diversity indices, we show that fast expansions and range shifts erode genetic diversity more than slow range expansions and range shifts. Our study provides analytical insight into the dynamics of travelling wave solutions in heterogeneous environments.
The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2,257 Europeans (the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared genomic segments, and used the lengths of these to infer the distribution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 10-50 genetic common ancestors from the last 1500 years, and upwards of 500 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since genetic ancestry is rare, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is substantial regional variation in the number of shared genetic ancestors: especially high numbers of common ancestors between many eastern populations likely date to the Slavic and/or Hunnic expansions, while much lower levels of common ancestry in the Italian and Iberian peninsulas may indicate weaker demographic effects of Germanic expansions into these areas and/or more stably structured populations. Recent shared ancestry in modern Europeans is ubiquitous, and clearly shows the impact of both small-scale migration and large historical events. Population genomic datasets have considerable power to uncover recent demographic history, and will allow a much fuller picture of the close genealogical kinship of individuals across the world.
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