Bulletin of the American Physical Society
APS March Meeting 2010
Volume 55, Number 2
Monday–Friday, March 15–19, 2010; Portland, Oregon
Session A27: Evolutionary and Ecological Systems |
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Sponsoring Units: DBP Chair: Jeff Gore, Massachusetts Institute of Technology Room: D137 |
Monday, March 15, 2010 8:00AM - 8:12AM |
A27.00001: Spontaneous Emergence of Modularity in an Evolving System: Nucleation of Biology from Chemistry Michael Deem, Jun Sun, Jiankui He We investigate the selective forces that promote the emergence of modularity in nature. We demonstrate the spontaneous emergence of modularity in a population of individuals that evolve in a changing environment. We show that the level of modularity correlates with the rapidity and severity of environmental change. The modularity arises as a synergistic response to the noise in the environment in the presence of horizontal gene transfer. We suggest that the hierarchical structure observed in the natural world may be a broken symmetry state, which generically results from evolution in a changing environment. To support our results, we analyze experimental protein interaction data and show that protein interaction networks became increasingly modular as evolution proceeded over the last four billion years. We also discuss a method to determine the divergence time of a protein. [Preview Abstract] |
Monday, March 15, 2010 8:12AM - 8:24AM |
A27.00002: Accelerated Evolution in the Death Galaxy Robert Austin, Chih-kuan Tung, Xiu-quing Gong, Guillaume Lambert, David Liao We recall 4 main guiding principles of evolution: 1) instability of defections, 2) stress induced non-random mutations, 3) genetic heterogeneity, and 4) fragmented populations. Our previous preliminary experiments have been relatively simple 1-D stress experiments. We are proceeding with 2-D experiments whose design is guided by these principles. Our new experiment we have dubbed the Death Galaxy because of it's use of these design principles. The ``galaxy'' name comes from the fact that the structure is designed as an interconnected array of micro-ecologies, these micro-ecologies are similar to the stars that comprise an astronomical galaxy, and provide the fragmented small populations. A gradient of the antibiotic Cipro is introduced across the galaxy, and we will present results which show how bacterial evolution resulting in resistance to Cipro is accelerated by the physics principles underlying the device. [Preview Abstract] |
Monday, March 15, 2010 8:24AM - 8:36AM |
A27.00003: Signatures of coevolution in protein superfamilies Sarosh Fatakia, Stefano Costanzi, Carson Chow Protein superfamilies, such as G protein-coupled receptors, consist of a large number of evolutionarily related proteins. A multiple sequence alignment (MSA) from such a superfamily can help identify signatures of evolution. A way to detect amino acid residues (AAs) that are important for the structure and/or function of proteins is to identify a cohort of AAs that evolve in tandem to compensate for mutations at any of those positions. To characterize such coevolutionary patterns, a MSA of homologous sequences was used to identify pairs of AA positions from the alignment having statistically significant mutual information (MI). Pairs of such MSA positions that had high MI were represented as a graph to show multiple associations. In that graph, the MSA positions represented vertices whose edges were linked if position pairs had high MI. The vertices with high degree were validated to be evolutionarily correlated positions that were important for structure and/or function. Using subsets of more recently evolved proteins from the diverse superfamily, most of those positions were determined to be under purifying selection. This comparative genomic analysis may help infer protein structure and coevolution in protein-protein interactions. [Preview Abstract] |
Monday, March 15, 2010 8:36AM - 8:48AM |
A27.00004: Correlation in the sequential evolutionary pattern of influenza hemagglutinin reveals its immunogenic and structural characters Keyao Pan, Michael Deem The immune system recognizes the hemagglutinin (HA) protein on the surface of the influenza virus. It is this protein that evolves to escape immune recognition. Correlation analysis is performed for all pairs of positions in the alignment of HA sequences collected in history. Spectral decomposition of the resulting matrix yields several independent eigenvectors that clusters those positions into several sectors, each of which corresponds to a subset of the positions and follows a relatively independent evolutionary pattern. Some of the obtained sectors match well with the five experimentally and statistically (using Shannon entropy) determined epitopes that are the sites of antibody binding. This result implies that different immunogenic epitopes of HA have characteristic patterns of escape mutation, arguably due to the distinct structures of the epitopes and properties of corresponding antibodies. In the three dimensional structure of HA, each sector is located in a compact surface region, thus the correlations in the evolution pattern occur locally in the tertiary structure. Novel sectors found, beyond the five known HA epitopes, may also possess certain biophysical functions. [Preview Abstract] |
Monday, March 15, 2010 8:48AM - 9:00AM |
A27.00005: The dynamics of gene duplication and transposons in microbial genome evolution Nicholas Chia, Nigel Goldenfeld Evidence indicates that new functional genes emerge from a process of gene duplication coupled with selection for a novel function. Recently, Bergthorsson et al. proposed a model of continuous selection in order to describe this process. Here, we examine their proposed evolutionary scheme, by modeling gene evolution using a stochastic simulation. Our results indicate that this model, and a related one that includes horizontal gene transfer, can account for the distribution of transposons in microbial genomes, and reproduce the observed environmentally-driven spatial dependence of transposon density in marine bacteria. [Preview Abstract] |
Monday, March 15, 2010 9:00AM - 9:12AM |
A27.00006: Growth mediated feedback and the abrupt onset of antibiotic resistance J. Barrett Deris Recent results in our lab indicate that global gene expression will change in a growth-dependent manner for bacteria in sublethal antibiotic levels. We analyzed a system containing a constitutively expressed drug resistance gene and found that growth-mediated feedback provided a mechanism for bistable growth rates. That is, two identical cell-lines in the same antibiotic-infused media may respond with distinct growth rates. Our experimental work with cells carrying this resistance gene has shown that a rapid drop in growth occurs over a relatively small range of antibiotic. This result is consistent with a growth plateau arising in our analysis of the feedback mechanism. Furthermore, experiments have shown that a culture's degree of drug resistance depends on the initial growth conditions prior to exposure to high levels of antibiotics. This result is consistent with the predicted existence of a hysteretic regime near the growth plateau. The work reveals concrete mechanisms by which bacteria cope with high levels of antibiotics and illustrates the importance of considering growth-mediated feedback on gene circuits. [Preview Abstract] |
Monday, March 15, 2010 9:12AM - 9:24AM |
A27.00007: Evolution of antibiotic resistance on a mesa-shaped fitness landscape Rutger Hermsen, Terence Hwa Rapid emergence of drug resistance is one of the biggest problems facing treatment of diseases ranging from bacterial infection to cancer. Recently it was found that, due to a novel growth-mediated positive feedback mechanism, the growth rate of bacteria exposed to sub-lethal antibiotic levels can drop abruptly when the drug level exceeds a sharp threshold (c.f.\ the preceding talk by Barrett Deris). This threshold level depends on the degree of expression and activity of the protein(s) providing antibiotic resistance. In environments with spatially varying antibiotic concentrations, this dependence gives rise to a mesa-shaped fitness landscape which provides a strong selective pressure for increasing the expression/activity of drug resistance near the cliff in the landscape. We have performed theoretical studies of evolution on such mesa-shaped fitness landscapes. These studies indicate a high rate of adaptation along the fitness cliff, often exceeding that of evolution on smooth fitness landscapes. The results of these studies establish a dynamic mechanism of evolution driven by a fitness cliff and environmental variability, and are conceptually distinct from the classical Darwinian notion of climbing a fitness gradient. [Preview Abstract] |
Monday, March 15, 2010 9:24AM - 9:36AM |
A27.00008: On-chip dynamic stress control for cancer cell evolution study Liyu Liu, Robert Austin The growth and spreading of cancer in host organisms is an evolutionary process. Cells accumulate mutations that help them adapt to changing environments and to obtain survival fitness. However, all cancer--promoting mutations do not occur at once. Cancer cells face selective environmental pressures that drive their evolution in stages. In traditional cancer studies, environmental stress is usually homogenous in space and difficult to change in time. Here, we propose a microfluidic chip employing embedded dynamic traps to generate dynamic heterogeneous microenvironments for cancer cells in evolution studies. Based on polydimethylsiloxane (PDMS) flexible diaphragms, these traps are able to enclose and shield cancer cells or expose them to external environmental stress. Digital controls for each trap determine the nutrition, antibiotics, CO2/O2 conditions, and temperatures to which trapped cells are subjected. Thus, the stress applied to cells can be varied in intensity and duration in each trap independently. The chip can also output cells from specific traps for sequencing and other biological analysis. Hence our design simultaneously monitors and analyzes cell evolution behaviors under dynamic stresses. [Preview Abstract] |
Monday, March 15, 2010 9:36AM - 9:48AM |
A27.00009: Modeling cell growth dynamics with a diffusion model of protein evolution Konstantin Zeldovich, Kelly Thayer Mesoscopic models of protein evolution, where mutations are represented as a diffusion process in protein stability space, gave important insight into the constraints on evolution imposed by protein thermodynamics in simple organisms such as bacteria or viruses. For example, the distribution of protein stablities and an absolute mutation rate limit directly follow from this model. Here, we propose a novel model, where the biomass growth rate of an individual cell is dependent on the stabilities of the cell's proteins, and the cell divides as soon as it reaches a critical biomass. Simulations of the model reveal that it reproduces all the features of the earlier models, including the mutation speed limit and the protein stability distribution, but adds a new dynamical dimension, a statistical description of the cell interdivision times which is extremely close to the experimental data. We analyze the dependence of the distribution of interdivision times on the mutation load and number of protein in the cell, and find that elevated mutation rates result in a broader distribution of interdivision times. Thus, we find that elevated mutation rates yield a disproportionately high fraction of very slow dividing cells, which may be a very important generic mechanism of non-adaptive resistance to mutagens. [Preview Abstract] |
Monday, March 15, 2010 9:48AM - 10:00AM |
A27.00010: Synthetic Yeast Cooperation Wenying Shou, Justin Burton Cooperation is wide-spread and has been postulated to drive major transitions in evolution. However, Darwinian selection favors ``cheaters'' that consume benefits without paying a fair cost. How did cooperation evolve against the threat of cheaters? To investigate the evolutionary trajectories of cooperation, we created a genetically tractable system that can be observed as it evolves from inception. The system consists of two engineered yeast strains -- a red-fluorescent strain that requires adenine and releases lysine and a yellow-fluorescent strain that requires lysine and releases adenine. Cells that consume but not supply metabolites would be cheaters. From the properties of two cooperating strains, we calculated and experimentally verified the minimal initial cell densities required for the viability of the cooperative system in the absence of exogenously added adenine and lysine. Strikingly, evolved cooperative systems were viable at 100-fold lower initial cell densities than their ancestors. We are investigating the nature and diversity of pro-cooperation changes, the dynamics of cooperator-cheater cocultures, and the effects of spatial environment on cooperation and cheating. [Preview Abstract] |
Monday, March 15, 2010 10:00AM - 10:12AM |
A27.00011: Emergence of Anisotropy in Flock Simulations and Its Computational Analysis Motohiro Makiguchi, Jun-ichi Inoue In real flocks, it was revealed that the angular density of nearest neighbors shows a strong {\it anisotropic structure} of individuals by very recent extensive field studies [Ballerini {\it et al}, {\it Proceedings of the National Academy of Sciences USA} {\bf 105}, pp. 1232-1237 (2008)]. In this paper, we show that this structure of anisotropy also emerges in an artificial flock simulation, namely, {\it Boid simulation} by Reynolds [C.W. Reynolds, {\it Flocks, Herds, and Schools: A Distributed Behavioral Model}, {\it Computer Graphics}, {\bf 21}, pp. 25-34 (1987)]. To quantify the anisotropy, we evaluate a useful statistics, that is to say, the so-called $\gamma$-value which is defined as an inner product between the vector in the direction of the lowest angular density of flocks and the vector in the direction of the flock is moving. Our results concerning the emergence of the anisotropy through the $\gamma$-value might enable us to judge whether an optimal flock simulation seems to be {\it realistic} or not. [Preview Abstract] |
Monday, March 15, 2010 10:12AM - 10:24AM |
A27.00012: Deriving hydrodynamic equations for the flocking dynamics of self-propelled agents Thomas Ihle, Alemayehu Gebremariam Hydrodynamic equations for interacting many-body systems follow, in principle, from microscopic laws. However, it is often difficult to quantitatively establish this link. Therefore, the general form of the macroscopic equations is usually obtained by symmetry arguments. We first study a particle-based model for fluid flow with a stochastic and discrete time evolution and show how the macroscopic transport equations can be rigorously derived from microscopic collision rules. The approach starts with the Liouville equation and leads to a multi-particle Enskog-equation which is treated by a Chapman-Enskog expansion. The same procedure is then applied to a simple model of self-propelled agents which mimick swarming birds. This model was proposed by T. Vicsek et al. [Phys. Rev. Lett. {\bf 75} (1995) 1226]; it has ``multi-particle collisions'' where birds within some interaction range align their flying directions. Spontaneous symmetry breaking leads to a global particle drift; the system is neither Galilean-invariant nor momentum conserving. The transition to global alignment of the flying birds is found to be continuous. We analyze the transition for small and large bird density, derive the hydrodynamic equations and perform a stability analysis of the flocking state. [Preview Abstract] |
Monday, March 15, 2010 10:24AM - 10:36AM |
A27.00013: Mobbing: a problem in flocking and deterrence M. Elias Tousley, Owen Glaze, Anna Schall, Suzanne Amador Kane We present experimental and theoretical studies of one type of mobbing behavior in which swarms of prey animals (e.g., tree swallows) harass a predator (e.g., a red-tailed hawk). Empirical field data were collected for tree swallows mobbing a fixed model predator; previous studies have established that this experimental design provokes the same response as actual ``perch-and-wait'' predator behavior. We extended these earlier studies using stereometric video to record the three-dimensional trajectories of prey birds and mobbing cries; we also analyzed single-angle video data taken of crows mobbing red-tailed hawks in flight. Video recordings of red-tailed hawk flight were filmed and analyzed to establish the dynamics of potential predator attacks. The trajectory analysis employed particle-tracking methods and statistical analyses to understand and model the dynamical rules governing this behavior. Swarming behavior during mobbing exhibited a high degree of periodicity and coordination both for fixed predator and in-flight mobbing attacks. The trajectories of individual mobbing birds were analyzed as a random walk superimposed on an approximately elliptical flightpath. Computer simulation studies reproduce several aspects of this behavior, in particular explaining how the mobbing strategy employed by prey birds minimizes the risk of hawk predation while optimizing the frequency of harassing attacks. [Preview Abstract] |
Monday, March 15, 2010 10:36AM - 10:48AM |
A27.00014: Robust ecological pattern formation induced by demographic noise Thomas Butler, Nigel Goldenfeld We demonstrate that demographic noise can induce persistent spatial pattern formation and temporal oscillations in the Levin-Segel predator-prey model for plankton-herbivore population dynamics. Although the model exhibits a Turing instability in mean field theory, demographic noise greatly enlarges the region of parameter space where pattern formation occurs. To distinguish between patterns generated by fluctuations and those present at the mean field level in real ecosystems, we calculate the power spectrum in the noise-driven case and predict the presence of fat tails not present in the mean field case. These results may account for the prevalence of large-scale ecological patterns, beyond that expected from traditional non-stochastic approaches. [Preview Abstract] |
Monday, March 15, 2010 10:48AM - 11:00AM |
A27.00015: Strong resonance explains cycles in sockeye salmon populations Christian Guill, Barbara Drossel The number of spawning sockeye salmon that return to their native streams in the Fraser river basin exhibit striking four-year oscillations, the dimension of which being no less notable than the widely known cycles of lynx and snowshoe hare in Canada. The period of the oscillation corresponds to the dominant generation time of these fish, and the phase differs between different stocks. Various not fully convincing explanations have been attempted, ascribing this phenomenon to transient effects, to stochastic influences, to depensatory predation, or to genetic effects. We show that these oscillations can be explained as a stable dynamical attractor of the population dynamics, resulting from a strong resonance near a Neimark Sacker bifurcation. This explains not only the long-term persistence of these oscillations, but also reproduces correctly the sequence of two strong years followed by two weak years. Furthermore, it explains the observations that the oscillations occur only in oligotrophic lakes, and that they do not occur in salmon species that have a longer generation time. [Preview Abstract] |
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