Session B63: Evolutionary and Ecological Dynamics II: Eco-evolutionary Feedback

Infect, replicate, and diffuse on: how bacteriophage grows and evolves during a spatial range expansion

Spatially growing populations are ubiquitous across scales, ranging from the human migration out of Africa to the spreading of diseases. In contrast to well-mixed populations where an individual’s chance of survival is only determined by its fitness, in spatially growing populations the physical location of an individual plays a crucial role: the individuals at the edge of the expanding front benefit from having access to virgin territory and giving their offspring the same advantage. The emerging population dynamic results in an evolutionary dynamic dominated by noise, with extreme consequences such as the accumulation of deleterious mutations at the population’s front.

To investigate how spatial range expansion affects the evolutionary dynamic of a population, we employ the bacteriophage T7-E. coli system. In an evolutionary experiment lasting only 7 days, we were able to evolve a T7 strain that more than doubled its spreading speed on a bacterial lawn compared to its ancestor. The seeming lack of accumulation of deleterious mutations at the front raised questions regarding the physical nature of the traveling wave describing the expansion front of T7, which was traditionally assumed to behave like a pulled wave at long time scales. In contrast to the assumptions used in the FKPP reaction-diffusion equation generating pulled waves, diffusion rate measurements show that phage dispersal is non-uniform along the range expansion since it depends on the local bacterial density. Using stochastic simulations, we find that this effect can have dramatic consequences on the phage genetic diversity at the front and on the adaptation potential of the population. The underlying physical origin of the effect broadens the relevance of our findings to a wide range of host-pathogen systems that share this feature.   

Dynamics of mtDNA populations in mammalian cells: role of mitochondrial dynamics and its interplay with mitochondrial membrane potential

Mitochondria are organelles found in almost all eukaryotic cells. They are highly dynamic and once formed, they can undergo changes in size and content via the processes of fusion, fission, and mitophagy. Mitochondria are famously known as the powerhouse of the cell for their role in cellular energy production. They are also essential for cell signaling and apoptosis, and have their own DNA, called mtDNA, which is maternally inherited. The same cell can have multiple variants of mtDNA, and harmful alterations in mtDNA can accumulate over time resulting in pathological changes in mitochondrial function and disease states. We develop and study a mathematical model to understand and predict the population dynamics of mtDNA and how it is correlated to changes in mitochondrial bioenergetics. We examine the spatiotemporal evolution of populations of healthy and dysfunctional mitochondria subject to mitochondrial biogenesis, fission, fusion, mitophagy, and changes in the mitochondrial membrane potential, and determine their relative impact on mtDNA population dynamics. Our results may provide insights into how different mtDNA populations survive and evolve under different selection pressures and the origins of mtDNA disorders.   

Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine

In nature microbial populations are subject to fluctuating nutrient levels. Nutrient fluctuations are important for evolutionary and ecological dynamics in microbial communities since they impact growth rates, population sizes, and biofilm formation. Here we show that when populations of Escherichia coli are subjected to cycles of nutrient excess (feasts) and scarcity (famine) their abundance dynamics during famines depend on the frequency and amplitude of feasts. We show that frequency and amplitude dependent dynamics in planktonic populations arise from nutrient and history dependent rates of aggregation and dispersal. These conclusions are enabled by precision measurements performed with automated continuous culture devices coupled to custom fluorescence microscopes. The instruments automatically sample, image and count single-cells drawn from continuously-cultured populations on a timescale of minutes for periods of weeks. The quality of the data enable us to construct a concise phenomenological model that recapitulates our experimental observations. Our results show that the statistical properties of environmental fluctuations have substantial impacts on spatial structure in bacterial populations driving large changes in abundance dynamics.   

Evolutionarily stable coexistence in a single nutrient: optimization and cross-feeding

Two questions on coexistence have perplexed community ecologists for nearly a century: first, the "paradox of the plankton", that nature world possess tremendous diversity while theoretical models suggested the number of species can hardly exceeds the number of nutrients. Second, evolution has been shown to exacerbate this paradox. As species are constantly evolving towards optimality, which may produce a supreme winner that takes over the habitat. To investigate these questions, we utilized and extended the graphical tools of resource-competition theory to relate and unify multiple models for microbial diversity, and quantified the optimal metabolic strategies in resource competition models in general. This framework was then applied to metabolic models that allows species to increase dimension in nutrient space by secreting metabolites. With this simple model, we explored the possibilities of coexistence though cross-feeding on a single supply nutrient, and investigated general criteria for such co-existence to be evolutionarily stable.   

Diversification of investment strategies in an ecological public goods game driven by the spatial structure of the population

Ecology and evolution work in tandem to create biodiversity, especially when they act on similar timescales, as can happen in microbial populations. Frequency and density dependent ecological models, like the public goods game, are known to be capable of supporting diverse populations. Recent experiments have shown diversification of gene expression in a bacterial population for a gene expressing a public good. Motivated by these observations we study an ecological public goods model and compare the extent to which mutations can fix in a population and generate diversity in a well-mixed situation and one with spatial structure. We show that rapid diversification within an ecological public goods game can drastically vary depending on the time scale of evolution and the time scale of ecological dynamics. While populations in a well-mixed model quickly come to equilibrium, limiting the amount of diversity typically to two dominant investment strategies; models with spatial structure prolong the time to equilibrium and allow multiple mutants to fix themselves in the population. Our theoretical studies agree with the experimental observations and point to a general principle how ecological public good games in spatially extended microbial population can lead to rapid diversification.
  

From Micro to Macro: Evolution of Novel Material Properties During the Transition to Multicellularity

The evolution of multicellular life from single-celled ancestors is one of the most radical shifts in the history of life on earth, and sets the stage for evolution of more complex life forms. Despite the significance of this transition, we know little about the process by which cells first assemble groups and form multicellular organisms. We study this problem experimentally; a single mutation in the ACE2 gene of Baker’s yeast S. cerevisiae prevents mother and daughter cells from separating after cellular division. These yeast clusters, called ‘snowflake’ yeast, comprise a few hundred cells and grow to a maximum diameter of 200 microns. To evolve larger multicellular size, snowflake yeast clusters must mitigate forces strong enough to fracture cell-cell bonds. After a year of artificial selection for larger multicellular size, five populations of snowflake yeast surprisingly evolved to grow to a maximum diameter of 1 mm. In this work we investigate how nascent multicellular clusters evolve to overcome substantial mechanical constraints and dramatically increase their size.
  

Universal Avalanche Fluctuations in Ecological communities under Resource Frustration

Avalanche critical fluctuations are an important dynamic feature of many systems including earthquakes and magnet polarization. They are caused by sudden release of potential built up by frustration in energy dissipation. Here, we introduce the concept of resource frustration in ecological systems to describe transient buildup of resources within a community which are then dissipated via avalanche-like events of individual species growth. We developed a general model to predict the conditions under which this type of fluctuations emerge in ecological systems and identified scaling laws and critical exponents of these avalanche events. We also demonstrated that these scaling laws are universal across multiple model microbial communities, (e.g., siderophore dependence and auxotrophic mutualism) using consumer-resource models. Our results reveal a novel class of transient phenomena in ecology and provide mechanisms by which stochastic fluctuations in individual components amplify and propagate throughout the ecological system.
  

Evolutionary Dynamics in a Group Population Structure with Barriers to Group Entry

The evolution of cooperation has been studied in many systems, from bacterial communities to human populations. It is well known that population structure is crucial to dynamics. For humans, group memberships are critical; we often interact with each other due to common group memberships. There exist network-based models to study human dynamics, but they generally do not allow for multiple group affiliations or incorporate barriers to group entry. We present a framework in which individuals interact through an evolutionary game with those who share their groups and update stochastically, with strategy and group memberships subject to evolutionary updating. We impose barriers to group entry based on group size. We find that with barriers, cooperation emerges, but it is most favored when we allow for the existence of "loners": a changing subset of individuals who spend a temporary "time-out" period not interacting with others. This work provides an analytical framework in which behavior in realistic population structures can be studied, and adds to a growing body of literature that recognizes the existence of loners as vital parts of systems.   

What do metabolic constraints inform us about the emergence of early stable bacterial communities?

Stability of an ecosystem is determined by its composition. As a system gains stability, one of the major trends observed during ecological succession, which refers to the development of a community, is an increase in compositional diversity [1]. It has been shown that multispecies systems can support a larger community with more surviving species at steady state when the variability across pairwise coupling strengths between species is smaller [2]. But how a small system with one species and no foreign invaders develops into a large diverse system remains an open question. Here, we consider the stability of a system under constant nutrient flux [3] when a species is competing with its closely related mutants to understand how early diversity is established. Using adiabatic approximation and discarding higher order terms, we recover the reduced dynamics for chemostats similar to Lotka-Volterra systems. By introducing small perturbations to the growth rates of the otherwise identical species constrained by rates of metabolic regulations, the rules for obtaining stable multispecies communities are obtained.

[1] E. P. Odum, Science 164, 262 (1969).
[2] G. Bunin, Physical Review E 95, (2017).
[3] A. Novick and L. Szilard, Proceedings of the National Academy of Sciences 36, 708 (1950).   

Eco-evolutionary hysteresis in bacterial genomes driven by horizontal gene transfer

Many naturally-occurring bacteria lead a lifestyle of metabolic dependency, i.e. they depend on others for crucial resources. We do not understand what factors drive bacteria towards this lifestyle, and how. Here, we systematically explain the role of horizontal gene transfer (HGT) in metabolic dependency evolution. Across 835 bacterial species, we mapped gene dynamics on a deep evolutionary tree, and assessed the impact of HGT and gene loss on bacterial metabolic networks. Our analyses suggest that genes acquired by HGT can affect which genes are later lost. Dependency evolution by gene loss is contingent on earlier HGT via two steps. First, we find that HGT and gene loss act on contrasting regions of metabolic networks—losses remove existing anabolic routes; HGT adds new catabolic routes. This increases the chance of new metabolic interactions between bacteria, which is a prerequisite for dependency evolution. Second, we show how gaining new routes can promote the loss of specific ancestral routes (termed "eco-evolutionary hysteresis", EEH). Phylogenetic patterns indicate that both types of dependencies—those mediated by EEH and pure gene loss—are equally likely. Our results highlight HGT as an important driver of metabolic dependency evolution in bacteria.   

Species Packing with Generalized Resource Dynamics

An important question in ecology is to understand how species assemble under different resource dynamics. Here we explored generalized MacArthur's resource models with two different resource dynamics: self-renewing(original MacArthur's) and external-supplied resource dynamics. A statistical physics inspired cavity method is used to solve two resource dynamics analytically. Surprisingly, we find that two resource dynamics have different upper bounds of species packing. We show that external-supplied resource dynamics can introduce higher order competition between species and affect coexistence patterns dramatically.   

Resource utilization determines growth rates and evolution in simple multi-species evolutionary model.

Species proliferate in an ecosystem if resources are abundant. Populous species at the same time deplete resources, which undermines their expansion. This suggests that resource utilization, appropriately quantified, should set their growth rate. By defining a species by the amount of different resources it consumes, and using the alignment of this vector with the vector of available resources as species growth rate, we can implement growth but also drift in species composition, and hence entire ecosystem evolution through speciation and adaptation. Our approach displays all the salient features of ecosystem evolution. We can evolve ecosystems even by initiating dynamics out of a single primordial ancestor. Despite the nonlinear and stochastic nature of this MacArthur-style approach, the modeling approach yields a robust, universal solution for the mean ecosystem fitness dynamics that is resilient against resource shocks. More generally, ecosystem fitness depends in an intuitive way on model parameters such as resource influx, reproduction rate and evolutionary noise. Our resource utilization approach to growth modeling so provides a general but simple starting point to evolutionary ecosystem dynamics.   

MEST-SPACETIME STRUCTURE, MASSENERGY STRUCTURE, AND ORIGIN of LIFE

MEST is a balance systemic model of mass, energy, space, and time.

According to Einstein field equation and negative Einstein equation, there are massenergy center with massenergy structure and spacetime center with spacetime structure which has gravity of the spacetime (as negative gravity).

The spacetime center structure can explain of dark matter and dark energy.
A balance structure between massenergy and spacetime can explain of the homogeneous, isotropic, and flat structure of the universe. It can suppose a balance system between the sun and a dark sun as a spacetime center of Oort cloud which is dark matter-dark energy.

Beginning of the solar system, there have dark matter around baby sun. The dark matter with ring structure (of spacetime center structure) impacted on the stellar matter with open structure, and create organic macromolecule of the life’s system with open system and closed system together. The impactions also could cause mass extinction, and could make natural gas, oil, and coals.

The period of the mass extinction has relationship with orbit of revolution of solar system, Galactic Spiral Arm, and balance system between sun and dark sun.
http://meetings.aps.org/Meeting/APR16/Session/M13.8