Bulletin of the American Physical Society
APS March Meeting 2013
Volume 58, Number 1
Monday–Friday, March 18–22, 2013; Baltimore, Maryland
Session B44: Focus Session: Population and Evolutionary Dynamics II |
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Sponsoring Units: DBIO GSNP Chair: Uwe Tauber, Virginia Tech Room: Hilton Baltimore Holiday Ballroom 1 |
Monday, March 18, 2013 11:15AM - 11:51AM |
B44.00001: The statistics of genetic diversity in rapidly adapting populations. Invited Speaker: Michael Desai Evolutionary adaptation is driven by the accumulation of beneficial mutations, but the sequence-level dynamics of this process are poorly understood. The traditional view is that adaptation is dominated by rare beneficial ``driver'' mutations that occur sporadically and then rapidly increase in frequency until they fix (a ``selective sweep''). Yet in microbial populations, multiple beneficial mutations are often present simultaneously. Selection cannot act on each mutation independently, but only on linked combinations. This means that the fate of any mutation depends on a complex interplay between its own fitness effect, the genomic background in which it arises, and the rest of the sequence variation in the population. The balance between these factors determines which mutations fix, the patterns of sequence diversity within populations, and the degree to which evolution in replicate populations will follow parallel (or divergent) trajectories at the sequence level. Earlier work has uncovered signatures of these effects, but the dynamics of genomic sequence evolution in adapting microbial populations have not yet been directly observed. In this talk, I will describe how full-genome whole-population sequencing can be used to provide a detailed view of these dynamics at high temporal resolution over 1000 generations in 40 adapting \textit{Saccharomyces cerevisiae }populations. This data shows how patterns of sequence evolution are driven by a balance between chance interference and hitchhiking effects, which increase stochastic variation in evolutionary outcomes, and the deterministic action of selection on individual mutations, which favors parallel solutions in replicate populations. [Preview Abstract] |
Monday, March 18, 2013 11:51AM - 12:03PM |
B44.00002: Metastability and Anomalous Fixation in Evolutionary Games on Scale-Free Networks Michael Assaf, Mauro Mobilia We study the influence of complex graphs on the metastability and fixation properties of a set of evolutionary processes. In the framework of evolutionary game theory, where the fitness and selection are frequency dependent and vary with the population composition, we analyze the dynamics of snowdrift games (characterized by a long-lived metastable coexistence state) on scale-free networks. Using an effective diffusion theory valid in the weak selection limit, we demonstrate how the scale-free structure affects the system's metastable state and leads to anomalous fixation. In particular, we analytically and numerically show that the probability and mean time to fixation are characterized by stretched-exponential behaviors with exponents depending on the network's degree distribution.\\[4pt] M. Assaf* and M. Mobilia*, PRL 109, 188701 (2012) (* - equal contribution) [Preview Abstract] |
Monday, March 18, 2013 12:03PM - 12:15PM |
B44.00003: Unveiling adaptation using high-resolution lineage tracking Jamie Blundell, Sasha Levy, Daniel Fisher, Dmitri Petrov, Gavin Sherlock Human diseases such as cancer and microbial infections are adaptive processes inside the human body with enormous population sizes: between $10^6 - 10^{12}$ cells. In spite of this our understanding of adaptation in large populations is limited. The key problem is the difficulty in identifying anything more than a handful of rare, large-effect beneficial mutations. The development and use of molecular barcodes allows us to uniquely tag hundreds of thousands of cells and enable us to track tens of thousands of adaptive mutations in large yeast populations. We use this system to test some of the key theories on which our understanding of adaptation in large populations is based. We (i) measure the fitness distribution in an evolving population at different times, (ii) identify when an appreciable fraction of clones in the population have at most a single adaptive mutation and isolate a large number of clones with independent single adaptive mutations, and (iii) use this clone collection to determine the distribution of fitness effects of single beneficial mutations. [Preview Abstract] |
Monday, March 18, 2013 12:15PM - 12:27PM |
B44.00004: Evolutionary dynamics of fluctuating populations with strong mutualism Thiparat Chotibut, David Nelson Evolutionary game theory with finite interacting populations is receiving increased attention, including subtle phenomena associated with number fluctuations, i.e., ``genetic drift.'' Models of cooperation and competition often utilize a simplified Moran model, with a strictly fixed total population size. We explore a more general evolutionary model with \textit{independent} fluctuations in the numbers of two distinct species [1], in a regime characterized by ``strong mutualism.'' The model has two absorbing states, each corresponding to fixation of one of the two species, and allows exploration of the interplay between growth, competition, and mutualism. When mutualism is favored, number fluctuations eventually drive the system away from a stable fixed point, characterized by cooperation, to one of the absorbing states. Well-mixed populations will thus be taken over by a single species in a finite time, despite the bias towards cooperation. We calculate both the fixation probability and the mean fixation time as a function of the initial conditions and carrying capacities in the strong mutualism regime, using the method of matched asymptotic expansions. Our results are compared to computer simulations.[1] S. Pigolotti et al., http://arxiv.org/abs/1208.4973 [Preview Abstract] |
Monday, March 18, 2013 12:27PM - 12:39PM |
B44.00005: Range expansions favor the evolution of cooperation in an experimental microbial metapopulation Manoshi Datta, Kirill Korolev, Ivana Cvijovic, Carmel Dudley, Jeff Gore Natural populations frequently undergo range expansions in response to changes in the environment. Recent work suggests that range expansions can have a strong effect on evolution, even leading to the fixation of deleterious alleles that would normally be outcompeted in the absence of migration. However, little is known about how range expansions might influence alleles under frequency- or density-dependent selection. Moreover, there is very little experimental evidence to complement existing theory, since expanding populations are difficult to study in nature. In this study, we have used a yeast experimental system to explore the effect of range expansions on the evolution of cooperative behaviors, which commonly display frequency- and density-dependent selection and are widespread in nature. We found that range expansions favor the evolution of cooperation in two ways: (1) through the enrichment of cooperators at the front of the expanding population, and (2) by allowing cooperators to ``outrun'' an invading wave of defectors. In this system, cooperation is enhanced through the coupling of population ecology and evolutionary dynamics in expanding populations, providing experimental evidence for a novel mechanism through which cooperative behaviors could be maintained in nature. [Preview Abstract] |
Monday, March 18, 2013 12:39PM - 12:51PM |
B44.00006: Slower recovery in space before collapse of connected populations Lei Dai, Kirill Korolev, Jeff Gore Slower recovery from perturbations near a tipping point and its indirect signatures in fluctuation patterns have been suggested to alert catastrophes in a wide variety of systems. Recent studies of populations in the field and in the laboratory have used time-series data to confirm some of the theoretically predicted early warning indicators, such as an increase in recovery time or in the size and timescale of fluctuations. However, the performance of warning signals in spatially extended systems remains to be examined empirically. Here we use spatially extended yeast populations, an experimental system displaying a fold bifurcation, to evaluate early warning signals based on spatio-temporal fluctuations and to identify a novel warning indicator in space. We found that two leading indicators based on fluctuations increased before collapse of connected populations; however, the magnitude of increase was smaller than that observed in isolated populations, possibly because local variation is reduced by dispersal. Furthermore, we propose a generic indicator based on deterministic spatial patterns, ``recovery length''. As the spatial counterpart of recovery time, recovery length is defined as the distance for connected populations to recover from perturbations in space (e.g. a region of poor quality). In our experiments, recovery length increased substantially before population collapse, suggesting that the spatial scale of recovery can provide a superior warning signal before tipping points in spatially extended systems. [Preview Abstract] |
Monday, March 18, 2013 12:51PM - 1:03PM |
B44.00007: Competitive Exclusion in Microbial Communities Charles Fisher, Pankaj Mehta The competitive exclusion principle of ecology suggests that two or more species cannot coexist in a community while living off of the same resources. Therefore, only species that occupy different niches can coexist. The process of community assembly is also heavily influenced by neutral drift due to stochastic birth, death and immigration of species. Currently, there is no consensus on the relative importance of ``niche'' and ``neutral'' processes in community assembly. We develop a stochastic birth-death-immigration model with competition for resources to examine the relative importance of these processes in microbial communities, and search for signatures of competitive exclusion in a large dataset of microbial community compositions containing relative species abundance data for thousands of environments. In addition, we discuss the role of metabolism in defining microbial niches. [Preview Abstract] |
Monday, March 18, 2013 1:03PM - 1:15PM |
B44.00008: Quantifying genetic diversity under a broad spectrum of deleterious mutations Benjamin Good, Michael Desai Recent studies have shown that selection against deleterious mutations may play a major role in shaping observed patterns of sequence variation in natural populations. However, our understanding of these patterns remains limited, since selection creates correlations along the genome that are difficult to disentangle from each other. Previous theoretical work has focused on the qualitative effects of selection on sequence diversity, using simplified models in which all selected mutations have the same fitness cost. Yet is known that deleterious mutations follow a wide distribution in most organisms, so it is necessary to extend our theoretical predictions to this more general case before we can make quantitative connections with existing data. The evolutionary dynamics of this regime are complicated: extant mutant lineages represent large, correlated fluctuations away from the background expectation, which hinders efforts to apply existing methods based on deterministic or ``mean-field'' approximations. Here, we will describe recent progress towards this goal, which is based on a ``coarse-graining'' of the underlying distribution of fitnesses in the population. [Preview Abstract] |
Monday, March 18, 2013 1:15PM - 1:27PM |
B44.00009: Cooperative Antibiotic Resistance in a Multi-Drug Environment Eugene Yurtsev, Lei Dai, Jeff Gore The emergence of antibiotic resistance in bacteria is a significant health concern. A frequent mechanism of antibiotic resistance involves the production of an enzyme which inactivates the antibiotic. By inactivating the antibiotic, resistant cells can ``share" their resistance with other cells in the bacterial population, suggesting that it may be possible to observe cooperation between strains that inactivate different antibiotics. Here, we experimentally track the population dynamics of two \emph{E. coli} strains in the presence of two different antibiotics. We find that together the strains are able to grow in antibiotic concentrations that inhibit growth of either of the strains individually. We observe that even when there is stable coexistence between the two strains, the population size of each strain can undergo large oscillations. We expect that our results will provide insight into the evolution of antibiotic resistance and the evolutionary origin of phenotypic diversity and cooperative behaviors. [Preview Abstract] |
Monday, March 18, 2013 1:27PM - 1:39PM |
B44.00010: Stochastic Loss of an Occasionally-Essential Function Elizabeth Jerison, Michael Desai Many biological functions are useful only in specific circumstances. For example, hundreds of single-gene deletions in yeast increase growth rate in some laboratory conditions. During periods of disuse, these genes are vulnerable to disruption or loss via random mutation and genetic drift. Yet they are maintained in natural populations, suggesting that they must be useful at least occasionally. Here we quantify the risk of loss of such occasionally-important functions. We focus on predicting how the statistics of environmental change determine the mean time to loss of the function. Our results suggest a refinement to the Savageau 'use-it-or-lose-it' principle of regulation, and put theoretical lower bounds on how often these functions must be necessary to the organism, in order to be maintained. [Preview Abstract] |
Monday, March 18, 2013 1:39PM - 1:51PM |
B44.00011: Rarely clicking Muller's ratchets Stephan Eule, Jakob Metzger In populations of finite size, weakly deleterious mutations can fix by chance. This phenomenon has been termed Muller's ratchet and one click of the ratchet refers to the loss of the fittest class of individuals with the fewest mutations. Despite the simplicity of the classical mathematical model of Muller's ratchet, surprisingly little is known in the biologically relevant regime where a click of the ratchet is a rare event. Here we show numerically that in this regime the rate of the ratchet strongly depends on the applied microscopic formulation (Wiright-Fisher/Moran) of the model, thus challenging the widely used diffusion approximation. Furthermore by employing a WKB-approximation in a simplified model, we obtain analytical results for the click rate, which agree well with the click rate of the full ratchet of the corresponding microscopical model. [Preview Abstract] |
Monday, March 18, 2013 1:51PM - 2:03PM |
B44.00012: Evolution of Bacterial Suicide Martin Tchernookov, Ilya Nemenman While active, controlled cellular suicide (autolysis) in bacteria is commonly observed, it has been hard to argue that autolysis can be beneficial to an \textit{individual} who commits it. We propose a theoretical model that predicts that bacterial autolysis is evolutionarily advantageous to an \textit{individual }and would fixate in physically structured environments for stationary phase colonies. We perform spatially resolved agent-based simulations of the model, which predict that lower mixing in the environment results in fixation of a higher autolysis rate from a single mutated cell, regardless of the colony's genetic diversity. We argue that quorum sensing will fixate as well, even if initially rare, if it is coupled to controlling the autolysis rate. The model does not predict a strong additional competitive advantage for cells where autolysis is controlled by quorum sensing systems that distinguish self from nonself. These predictions are broadly supported by recent experimental results in \textit{B. subtilis }and \textit{S. pneumoniae.} [Preview Abstract] |
Monday, March 18, 2013 2:03PM - 2:15PM |
B44.00013: Experimental Insights into Collective Effects in Eukaryotic Cell Proliferation in Dilute Suspensions Carl Franck, Igor Segota, Ariana Strandburg-Peshkin, Xiao-Qiao S. Zhou, Archana Rachakonda, Benjamin Yavitt, Catherine J. Lussenhop, Sungsu Lee, Kevin Tharratt, Amrish Deshmukh, Elisabeth Sebesta, Myron Zhang, Sharon Lau, Sarah Bennedsen, David Franck, Viyath Fernando, Junseok Oh Physicists can look to dilute suspensions of apparently solitary cells in suspension for elegant realizations of multicellular behavior. In contrast to our earlier work (Phys. Rev. E v. 77, 041905 (2008)) with the amoeba Dictyostelium discoideum we are discovering that the vital intercellular communications responsible for the well-known but poorly understood slow to fast transition in a growing culture as a function of time might be due to the passage of chemical messages between transient cell clusters or throughout the entire system as opposed to binary collisions. In considering the observed variation in proliferation rates we have been surprised to discover that for best growth cultures are much more dependent on incubator geometry than previously suspected. [Preview Abstract] |
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