Bulletin of the American Physical Society
APS March Meeting 2014
Volume 59, Number 1
Monday–Friday, March 3–7, 2014; Denver, Colorado
Session B12: Invited Session: Exploring the Dynamics of Evolution and Ecology of Biological Systems |
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Sponsoring Units: DBIO GSNP Chair: Alexandre Morozov, Rutgers University Room: 205 |
Monday, March 3, 2014 11:15AM - 11:51AM |
B12.00001: Exploring the Dynamics of Evolution and Ecology of Biological Systems Invited Speaker: Jin Wang We established the potential and flux landscape theory for evolution. We found explicitly the conventional Wright's gradient adaptive landscape based on the mean fitness is inadequate to describe the general evolutionary dynamics. We show the intrinsic potential as being Lyapunov function (monotonically decreasing in time) does exist and can define the adaptive landscape for general evolution dynamics for studying global stability. The driving force determining the dynamics can be decomposed into gradient of potential landscape and curl probability flux. Non-zero flux causes detailed balance breaking and measures how far the evolution from equilibrium state. The gradient of intrinsic potential and curl flux are perpendicular to each other in zero fluctuation limit resembling electric and magnetic forces on electrons. We quantified intrinsic energy, entropy and free energy of evolution and constructed non-equilibrium thermodynamics. The intrinsic non-equilibrium free energy is a Lyapunov function. Both intrinsic potential and free energy can be used to quantify the global stability and robustness of evolution. We investigated an example of three allele evolutionary dynamics with frequency dependent selection (detailed balance broken). We uncovered the underlying single, triple, and limit cycle attractor landscapes. We found quantitative criterions for stability through landscape topography. We also quantified evolution pathways and found paths do not follow potential gradient and are irreversible due to non-zero flux. We generalized the original Fisher's fundamental theorem to the general (i.e., frequency dependent selection) regime of evolution by linking the adaptive rate with not only genetic variance related to the potential but also the flux. We show there is an optimum potential where curl flux resulting from biotic interactions of individuals within a species or between species can sustain an endless evolution even if the physical environment is unchanged. We offer a theoretical basis for explaining the corresponding Red Queen hypothesis proposed by Van Valen. Our work provides a theoretical foundation for evolutionary dynamics. [Preview Abstract] |
Monday, March 3, 2014 11:51AM - 12:27PM |
B12.00002: Genetic constraints on adaptive evolution in principle and in practice Invited Speaker: Daniel Weinreich ~~Geneticists have long recognized that pairs of mutations often produce surprising effects on the organism, given their effects in isolation. Such mutational interactions are called epistasis. Importantly, epistasis among mutations influencing an organism's survival or reproductive success can constrain the temporal order in which mutations will be favored by natural selection. After exploring these theoretical considerations more fully, we will demonstrate substantial epistatic constraint on the evolution of an enzyme that confers bacterial antibiotic resistance. Such epistatically induced constraints turn out to be rather common in enzyme evolution, and we will briefly discuss recent work that seeks to explicate its mechanistic basis using methods of molecular and structural biology. Finally we observe that the epistatic interaction between two mutations itself often varies with genetic context, implying the existence of higher-order interactions. We present a computational framework for assessing magnitude of epistatic interactions of all orders, and show that non-negligible epistatic interactions of all orders are common in a diverse set of biological systems. [Preview Abstract] |
Monday, March 3, 2014 12:27PM - 1:03PM |
B12.00003: A biophysical perspective on molecular evolution Invited Speaker: Claus Wilke The field of molecular evolution investigates how genes and genomes evolve over time. It has its origin in the late 1960s, when the first DNA and protein sequences were becoming available. With rapid progress in sequencing technologies came ever increasing demand for computational tools to study molecular evolution. Today, molecular evolution is among the largest subfields of evolutionary biology, and arguably one of the most computationally advanced. A side effect of the strong emphasis on developing sophisticated methods for sequence analysis has been that the underlying biophysical objects represented by the sequences, DNA molecules, RNA molecules, and proteins, have taken a back-seat in much computational molecular-evolution work. The vast majority of algorithms for sequence analysis, for example, operate purely on strings of letters, and don't incorporate any information of the biophysical reality that these letters represent. However, DNA, RNA, and proteins are three-dimensional physical objects composed of many interacting particles. We thus expect that their genetic evolution over time is shaped to some extent by these physical properties. Here, I will discuss the extent to which biophysical properties of proteins shape genetic evolution, and how we can use these properties to improve evolutionary analyses. [Preview Abstract] |
Monday, March 3, 2014 1:03PM - 1:39PM |
B12.00004: Acceleration of Evolutionary Spread by Long-Range Dispersal Invited Speaker: Oskar Hallatschek The spreading of evolutionary novelties across populations is the central element of adaptation. Unless population are well-mixed (like bacteria in a shaken test tube), the spreading dynamics not only depends on fitness differences but also on the dispersal behavior of the species. Spreading at a constant speed is generally predicted when dispersal is sufficiently short-ranged. However, the case of long-range dispersal is unresolved: While it is clear that even rare long-range jumps can lead to a drastic speedup, it has been difficult to analyze the ensuing stochastic growth process. We present a simple self-consistent argument supported by simulations that accurately predicts evolutionary spread for broad distributions of long distance dispersal. In contrast to the exponential laws predicted by deterministic ``mean-field'' models, spread is either according to a super-linear power-law or a stretched exponential law, depending on the tails of the dispersal kernel. Fluctuations and the relation to supercritical long-range percolation are discussed. Due to the simplicity of our model, which lacks any complex interactions between individuals, we expect our results to be applicable to a wide range of spreading processes. Our results may be used, in particular, to estimate the spread of modern human epidemics, which are greatly accelerated by the human aviation. Based on joint work with Daniel S. Fisher, Stanford. [Preview Abstract] |
Monday, March 3, 2014 1:39PM - 2:15PM |
B12.00005: Experimental evolution and epistasis in variable environments Invited Speaker: Sander Tans Environmental changes trigger cellular responses, but also impose selective pressures on the underlying regulatory systems. To disentangle this complex interplay we follow a synthetic biology approach. By linking the output of regulatory systems to bacterial growth, quantified temporally variable selective pressures can be applied to regulatory systems. This approach allows one to explore how networks evolve in complex variable environments. Epistatic interactions that underlie evolutionary constraint have mainly been studied for constant external conditions. However, environmental changes may modulate epistasis and hence affect genetic constraints. We investigate genetic constraints in the adaptive evolution of a novel regulatory function in variable environments, using the lac repressor, LacI, as a model system. We systematically reconstructed mutational trajectories from wild type LacI to three different variants that each exhibit an inverse response to the inducing ligand IPTG, and analyzed the higher-order interactions between genetic and environmental changes. We find epistasis to depend strongly on the environment. As a result, mutational steps essential to inversion but inaccessible by positive selection in one environment, become accessible in another. We present a graphical method to analyze the observed complex higher-order interactions between multiple mutations and environmental change, and show how they can be explained by a combination of mutational effects on allostery and thermodynamic stability. This dependency of genetic constraint on the environment should fundamentally affect evolutionary dynamics and phylogenetic analysis. [Preview Abstract] |
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