Bulletin of the American Physical Society
APS March Meeting 2018
Volume 63, Number 1
Monday–Friday, March 5–9, 2018; Los Angeles, California
Session V49: Evolutionary Systems Biology IFocus
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Sponsoring Units: DBIO GSNP Chair: Daniel Charlebois, State Univ of NY- Stony Brook Room: LACC 511A |
Thursday, March 8, 2018 2:30PM - 3:06PM |
V49.00001: Protein Evolution Under Multiple Opposing Selection Factors Invited Speaker: Erdal Toprak Models of evolutionary dynamics often focus on trajectories of variation due to a specific condition of selection, but the natural process often involves multiple, potentially opposing selection pressures. Understanding the strategies for variation in the context of complex selection pressures is critical for both basic and applied biomedical science. To better understand evolutionary dynamics under complex selection conditions, we will focus on three questions using a bacterial membrane protein as a model system: |
Thursday, March 8, 2018 3:06PM - 3:18PM |
V49.00002: Predominance of Positive Epistasis Among Resistance-Associated Mutations in HIV-1 Protease Lei Dai, Tianhao Zhang, John Barton, Arup Chakraborty, James Lloyd-Smith, Ren Sun Drug-resistant mutations often have deleterious impacts on replication fitness of viruses, posing a fitness barrier that can only be overcome by compensatory mutations. However, the importance of fitness barriers in the evolution of HIV-1 drug resistance is not evident in clinical samples or traditional in vitro selection experiments, as these data only capture the overall outcome of selection. In this study, we systematically profile the fitness effects of resistance-associated mutations in HIV-1 protease using deep mutational scanning. As expected, we find that the majority of resistance-associated mutations have significantly deleterious effects on viral replication. However, in contrast to the common belief in protein evolution that deleterious mutations tend to interact negatively, we observe the dominance of positive epistasis among resistance-associated mutations in HIV-1 protease. Furthermore, we applied the Potts model on HIV sequence data from patients to infer the genetic interactions. The Potts model also suggests that positive epistasis is significantly enriched among resistance-associated mutations. Overall, our results provide valuable insights to the role of fitness barriers and positive epistasis in the evolution of drug resistance. |
Thursday, March 8, 2018 3:18PM - 3:30PM |
V49.00003: Thermodynamics and Statistical Mechanics of Viral Evolution Beyond Equilibrium Barbara Jones, Greyson Lewis, Wallace Marshall We study a model of viral evolution, in which viruses have a barrier to cell entry, mediated by their match to cell “key”, followed by a viral-type dependent immune response by the cell, and finally a probability to reproduce and mutate. These mutated viruses then go on to attack other cells in the model. Previously we found equilibrium behavior, featuring a phase transition as a function of temperature and immunity [PLOS One 2015 https://doi.org/10.1371/journal.pone.0137482]. Here we describe our studies of the behavior of this model as a dynamical system, and the nonequilibrium evolution of the quasispecies distribution including metastable states and other unexpected features. |
Thursday, March 8, 2018 3:30PM - 3:42PM |
V49.00004: Bet Hedging over Growth and Survival under Demographic Fluctuations BingKan Xue, Stanislas Leibler The growth of biological populations is subject to stochastic fluctuations in the birth and death processes of individuals. Such demographic fluctuations create a trade-off between growth and survival for small populations. During biological dispersal, for example, the survival of newly founded populations may be as important as the growth of already established populations. Using a statistical physics model of birth, death, and migration processes, we show that the expansion rate of a species' overall abundance can be maximized by a bet-hedging strategy, in which the population constantly diversifies into subpopulations of “fast-growing” and “better-surviving” individuals. A similar bet-hedging strategy has previously been suggested as a defense mechanism against environmental variations. We unify those bet-hedging strategies against demographic and environmental variations as a general means of adaptation to both types of uncertainties in population growth. |
Thursday, March 8, 2018 3:42PM - 3:54PM |
V49.00005: Changing Fitness Landscapes During Host-Parasite Coevolution Opens Adaptive Pathways to Evolutionary Novelty Animesh Gupta, Justin Meyer It has been proposed that the evolution of new functions can be explained by host-parasite coevolution. Experiments on a virus, bacteriophage lambda, and its host, Escherichia coli, have accordingly shown that lambda evolves to exploit a novel receptor during their coevolution. The importance of coevolution for the innovation, however, was not directly tested. We provide a comprehensive analysis of the process of adaptation leading to evolutionary novelty in this model system by measuring lambda’s fitness landscape with a new high throughput technology (MAGE-Seq). The innovation in lambda was thought to be triggered by the evolution of host resistance, which was expected to deform lambda’s landscape in ways to open adaptive pathways. As predicted, the landscape measured with wild type cells was significantly different than when measured with evolved resistant host cells. However, this initial hypothesis turned out to be overly simple. Simulations of lambda populations evolving on the landscapes, along with additional experiments, showed that paths to the innovation required evolving first on the wild type host, and then on the evolved host. Altogether, we provide definitive evidence that coevolutionary dynamics can lead to evolutionary innovations. |
Thursday, March 8, 2018 3:54PM - 4:06PM |
V49.00006: Ecological conditions enabling the evolution of the multiplicity of infection dependent lysogenic decision of phage lambda Michael Cortes, Gabor Balazsi, Jonathan Krog Theories on phage lambda's lysogenic decision suggest that by allocating a subpopulation of infections to the dormant lysogenic state, survival of the population is ensured through uncertain deleterious environments. For lambda, lysogenization increases with the number of infecting phages, a quantity called the multiplicity of infection or MOI. However, theory predicts enhanced survival if lysogenization was independent of, or decreased with, MOI so long as some percentage of infections result in lysogeny. Using agent-based modeling, we compete phage strains with different MOI-dependencies against each other in variable environments. We discover that certain MOI-dependencies can be naturally selected over others, suggesting that evolution quantitatively tuned lambda's MOI-dependence to maximize survival. |
Thursday, March 8, 2018 4:06PM - 4:42PM |
V49.00007: Quantitative single cell biophysics: Unraveling bacterial adaptation dynamics under fluctuating environments Invited Speaker: Guillaume Lambert
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Thursday, March 8, 2018 4:42PM - 4:54PM |
V49.00008: Cooperative mechanical effects hinder natural selection in dense cellular populations Carl Schreck, Jona Kayser, Diana Fusco, Matti Gralka, Oskar Hallatschek Many cellular populations exist in a densely packed state where cells must physically push aside their neighbors in order to proliferate. Using S. cerivisiae experiments and computational models, we show that these growth-induced forces generate an effective surface-tension that flattens the surface of expanding colonies. This effective surface tension couples the evolutionary fate of phenotypes across mesoscopic length-scales, strongly attenuating selective efficiency in comparison to previous non-mechanical spatial models. As a consequence, deleterious (slower growing) mutants are purged from the population much more slowly than predicted by previous models. We show that this slow purging facilitates the rescue of costly alleles upon a subsequent adaptive gain. Due to its purely mechanical nature, we expect this effect to be present in a wide range of sufficiently dense cellular populations. Our finding is particularly relevant to the emergence of antibiotic resistance, where mechanical-attenuated selection is expected to promote the emergence of drug resistant phenotypes associated with a fitness cost prior to treatment. |
Thursday, March 8, 2018 4:54PM - 5:06PM |
V49.00009: Cross-species investigation of the mechanisms driving a period-doubling bifurcation in voltage and calcium dynamics of paced cardiac tissue Conner Herndon, Flavio Fenton Much research has been devoted to investigating the initiation of cardiac arrhythmias by alternans, a period doubling bifurcation in the duration of cardiac action potentials which is strongly correlated with the onset of sudden cardiac death. Alternans results from a cellular level instability in the bidirectionally coupled voltage and calcium dynamics. Although the formation and maintenance of alternans has been studied extensively in animal models such as rabbit, rat, and zebrafish, surprisingly little attention has been given to the discrepancies observed across species. Even when the hearts of two species are anatomically similar, the electrophysiology can behave quite differently. In this talk I will present high spatiotemporal resolution optically mapped fluorescent recordings of transmembrane voltage and intracellular calcium transients from the surfaces of Langendorff-perfused whole hearts of a variety of species including rabbit, porcine, canine, cat, rat, zebrafish, alligator, and snake. I will discuss the variety of alternans observed in these species and the driving mechanisms. Furthermore, I will present a minimal cardiac cell model that reproduces the observed alternans dynamics when coupled in tissue. |
Thursday, March 8, 2018 5:06PM - 5:18PM |
V49.00010: Quantitative analysis of the diversity of the “picture-wing” family of Drosophila Vasyl Alba, Madhav Mani It is believed that large diversity of nearly 1000 Hawaiian Drosophila originated from a single species, which makes this family of Drosophila system is a prominent example of an adaptive radiation. These species, the “picture-wing” family, have reach variety of patterns on their wings. We develop quantitative methods to analyze the diversity of their wing patterns, that is insensitive to the particular size of the wing. We use our analysis to address questions pertaining to evolution of patterning. |
Thursday, March 8, 2018 5:18PM - 5:30PM |
V49.00011: Physical Influence on the Trajectory of Nascent Multicellular Evolution Shane Jacobeen, Thomas Day, Elyes Graba, Colin Brandys, Jennifer Pentz, David Yanni, William Ratcliff, Peter Yunker The evolution of multicellularity transformed life on earth by setting the stage for all higher orders of organismal complexity; yet many critical aspects of this transition remain poorly understood. Using experimental evolution of snowflake yeast1,2, we study the role of physics in this fundamental evolutionary process. Under selection for large size, nascent multicellular snowflake yeast clusters evolve increased fitness along trajectories that are highly physically efficient. Further, we find that a physically challenging environment impedes the evolution of increased cluster fitness. Thus we demonstrate the significant role played by physical constraints in the evolution of nascent multicellularity. |
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