Biology subjects

Doebeli, M.

Publications and source records attributed to Doebeli, M..

13 recordsLinked to original sources

bioRxiv2024

Evolutionary branching in multi-level selection models

We study a model of group-structured populations featuring individual-level birth and death events, and group-level fission and extinction events. Individuals play games within their groups, while groups play games against other groups. Pay-offs from individual-level games affect birth rates of individuals, and payoffs from group-level games affect group extinction rates. We focus on the the evolutionary dynamics of continuous traits with particular emphasis on the phenomenon of evolutionary diversification. Specifically, we consider two-level processes in which individuals and groups play continuous snowdrift or prisoners dilemma games. Individual game strategies evolve due to selection pressure from both the individual and group level interactions. The resulting evolutionary dynamics turns out to be very complex, including branching and type-diversification at one level or the other. We observe that a weaker selection pressure at the individual level results in more adaptable groups and sometimes group-level branching. Stronger individual-level selection leads to more effective adaptation within each group while preventing the groups from optimizing their strategies for group-level games.

evolutionary biology↗

bioRxiv2022

Adaptive diversification and niche packing on rugged fitness landscapes

Explaining the emergence of diversity and the coexistence of competing types has long been one of the main goals of ecological theory. Rugged fitness landscapes have often been used to explain diversity through the presence of local peaks, or adaptive zones, in the fitness landscape acting as available niches for different species. Alternatively, niche-packing and theories based on limiting similarity describe frequency-dependent selection leading to the organic differentiation of a continuous phenotype space into multiple coexisting types. By combining rugged carrying capacity landscapes with frequency-dependent selection, here we investigate the effects of ruggedness on adaptive diversification and stably maintained diversity. We show that while increased ruggedness often leads to a decreased opportunity for adaptive diversification, it is the shape of the global carrying capacity function, not the local ruggedness, that determines the diversity of the ESS and the total diversity a system can stably maintain.

evolutionary biology↗

bioRxiv2022

Ecological diversity exceeds evolutionary diversity in model ecosystems

Understanding community saturation is fundamental to ecological theory. While investigations of the diversity of evolutionary stable states (ESSs) are widespread, the diversity of communities that have yet to reach an evolutionary endpoint is poorly understood. We use Lotka-Volterra dynamics and trait-based competition to compare the diversity of randomly assembled communities to the diversity of the ESS. We show that, with a large enough founding diversity (whether assembled at once or through sequential invasions), the number of long-time surviving species exceeds that of the ESS. However, the excessive founding diversity required to assemble a saturated community increases rapidly with the dimension of phenotype space. Additionally, traits present in communities resulting from random assembly are more clustered in phenotype space compared to random, though still markedly less ordered than the ESS. By combining theories of random assembly and ESSs we bring a new viewpoint to both the saturation and random assembly literature.

ecology↗

bioRxiv2021

Phenotypic heterogeneity is adaptive for microbial populations under starvation

To persist in variable environments populations of microorganisms have to survive periods of starvation and be able to restart cell division in nutrient-rich conditions. Typically, starvation signals initiate a transition to a quiescent state in a fraction of individual cells, while the rest of the cells remain non-quiescent. It is widely believed that, while quiescent cells (Q) help the population to survive long starvation, the non-quiescent cells (NQ) are a side effect of imperfect transition. We analysed regrowth of starved monocultures of Q and NQ cells compared to mixed, heterogeneous cultures in simple and complex starvation environments. Our experiments, as well as mathematical modelling, demonstrate that Q monocultures benefit from better survival during long starvation, and from a shorter lag phase after resupply of rich medium. However, when the starvation period is very short, the NQ monocultures outperform Q and mixed cultures, due to their short lag phase. In addition, only NQ monocultures benefit from complex starvation environments, where nutrient recycling is possible. Our study suggests that phenotypic heterogeneity in starved populations could be a form of bet hedging, which is adaptive when environmental determinants, such as the length of the starvation period, the length of the regrowth phase, and the complexity of the starvation environment vary over time. ImportanceNon-genetic cell heterogeneity is present in glucose starved yeast populations in the form of quiescent (Q) and nonquiescent (NQ) phenotypes. There is evidence that Q cells help the population to survive long starvation. However, the role of the NQ cell type is not known, and it has been speculated that the NQ phenotype is just a side effect of imperfect transition to the Q phenotype. Here we show that, in contrast, there are ecological scenarios in which NQ cells perform better than monocultures of Q cells or naturally occuring mixed populations containing both Q and NQ. NQ cells benefit when the starvation period is very short and environmental conditions allow nutrient recycling during starvation. Our experimental and mathematical modeling results suggest a novel hypothesis: the presence of both Q and NQ phenotypes within starved yeast populations may reflect a form of bet hedging, where different phenotypes provide fitness advantages depending on environmental conditions.

evolutionary biology↗

bioRxiv2021

Origin of diversity in spatial social dilemmas

Cooperative investments in social dilemmas can spontaneously diversify into stably co-existing high and low contributors in well-mixed populations. Here we extend the analysis to emerging diversity in (spatially) structured populations. Using pair approximation we derive analytical expressions for the invasion fitness of rare mutants in structured populations, which then yields a spatial adaptive dynamics framework. This allows us to predict changes arising from population structures in terms of existence and location of singular strategies, as well as their convergence and evolutionary stability as compared to well-mixed populations. Based on spatial adaptive dynamics and extensive individual based simulations, we find that spatial structure has significant and varied impacts on evolutionary diversification in continuous social dilemmas. More specifically, spatial adaptive dynamics suggests that spontaneous diversification through evolutionary branching is suppressed, but simulations show that spatial dimensions offer new modes of diversification that are driven by an interplay of finite-size mutations and population structures. Even though spatial adaptive dynamics is unable to capture these new modes, they can still be under-stood based on an invasion analysis. In particular, population structures alter invasion fitness and can open up new regions in trait space where mutants can invade, but that may not be accessible to small mutational steps. Instead, stochastically appearing larger mutations or sequences of smaller mutations in a particular direction are required to bridge regions of unfavourable traits. The net effect is that spatial structure tends to promote diversification, especially when selection is strong.

evolutionary biology↗

bioRxiv2021

Multilevel selection favors fragmentation modes that maintain cooperative interactions in multispecies communities

Reproduction is one of the requirements for evolution and a defining feature of life. Yet, across the tree of life, organisms reproduce in many different ways. Groups of cells (e.g., multicellular organisms, colonial microbes, or multispecies biofilms) divide by releasing propagules that can be single-celled or multicellular. What conditions determine the number and size of reproductive propagules? In multicellular organisms, existing theory suggests that single-cell propagules prevent the accumulation of deleterious mutations (e.g., cheaters). However, groups of cells, such as biofilms, sometimes contain multiple metabolically interdependent species. This creates a reproductive dilemma: small daughter groups, which prevent the accumulation of cheaters, are also unlikely to contain the species diversity that is required for ecological success. Here, we developed an individual-based, multilevel selection model to investigate how such multi-species groups can resolve this dilemma. By tracking the dynamics of groups of cells that reproduce by fragmenting into smaller groups, we identified fragmentation modes that can maintain cooperative interactions. We systematically varied the fragmentation mode and calculated the maximum mutation rate that communities can withstand before being driven to extinction by the accumulation of cheaters. We find that for groups consisting of a single species, the optimal fragmentation mode consists of releasing single-cell propagules. For multi-species groups we find various optimal strategies. With migration between groups, single-cell propagules are favored. Without migration, larger propagules sizes are optimal; in this case, group-size dependent fissioning rates can prevent the accumulation of cheaters. Our work shows that multi-species groups can evolve reproductive strategies that allow them to maintain cooperative interactions. Author summaryIn order to reproduce, multicellular organisms and colonial bacteria fragment into offspring groups. Fragmentation modes in nature are very diverse: e.g. some organisms split into two halves, while others release single-celled propagules. These fragmentation modes can have fitness consequences, e.g. small propagules reduce the spread of deleterious mutants. However, the consequences of different fragmentation modes are not yet well understood for groups of cells containing several metabolically interdependent species, such as complex biofilms. We developed a multilevel selection model to investigate the effect of fragmentation mode on the accumulation of deleterious mutants when groups contain multiple species. In such groups, small propagules are not always a viable strategy, because they may harbor low species diversity. We find that alternative mechanisms, such as migration of cells between groups and group-size dependent fissioning rates, can prevent the accumulation of mutants. We also find that multilevel selection can lead to the evolution of fragmentation strategies that allow multi-species groups to thrive in the face of deleterious mutations.

evolutionary biology↗

bioRxiv2021

Evolution to alternative levels of stable diversity leaves areas of niche space unexplored

One of the oldest and most persistent questions in ecology and evolution is whether natural communities tend to evolve toward saturation and maximal diversity. Robert MacArthurs classical theory of niche packing and the theory of adaptive radiations both imply that populations will diversify and fully partition any available niche space. However, the saturation of natural populations is still very much an open area of debate and investigation. Additionally, recent evolutionary theory suggests the existence of alternative evolutionary stable states (ESSs), which implies that some stable communities may not be fully saturated. Using models with classical Lokta-Volterra ecological dynamics and three formulations of evolutionary dynamics (a model using adaptive dynamics, an individual-based model, and a partial differential equation model), we show that following an adaptive radiation, communities can often get stuck in low diversity states when limited by mutations of small phenotypic effect. These low diversity metastable states can also be maintained by limited resources and finite population sizes. When small mutations and finite populations are considered together, it is clear that despite the presence of higher-diversity stable states, natural populations are likely not fully saturating their environment and leaving potential niche space unfilled. Additionally, within-species variation can further reduce community diversity from levels predicted by models that assume species-level homogeneity. Author summaryUnderstanding if and when communities evolve to saturate their local environments is imperative to our understanding of natural populations. Using computer simulations of classical evolutionary models, we study whether adaptive radiations tend to lead toward saturated communities, in which no new species can invade or remain trapped in alternative, lower diversity stable states. We show that with asymmetric competition and small effect mutations, evolutionary Red Queen dynamics can trap communities in low diversity metastable states. Moreover, limited resources not only reduces community population sizes, but also reduces community diversity, denying the formation of saturated communities and stabilizing low diversity, non-stationary evolutionary dynamics. Our results are directly relevant to the longstanding questions important to both ecological empiricists and theoreticians on the species packing and saturation of natural environments. Also, by showing the ease evolution can trap communities in low diversity metastable states, we demonstrate the potential harm in relying solely on ESSs to answer questions of biodiversity.

evolutionary biology↗

bioRxiv2020

Boom-bust population dynamics can increase diversity in evolving competitive communities

The processes and mechanisms underlying the origin and maintenance of biological diversity have long been of central importance in ecology and evolution. The competitive exclusion principle states that the number of coexisting species is limited by the number of resources, or by the species similarity in resource use. Natural systems such as the extreme diversity of unicellular life in the oceans provide counter examples. It is known that mathematical models incorporating population fluctuations can lead to violations of the exclusion principle. Here we use simple eco-evolutionary models to show that a certain type of population dynamics, boom-bust dynamics, can allow for the evolution of much larger amounts of diversity than would be expected with stable equilibrium dynamics. Boom-bust dynamics are characterized by long periods of almost exponential growth (boom) and a subsequent population crash due to competition (bust). When such ecological dynamics are incorporated into an evolutionary model that allows for adaptive diversification in continuous phenotype spaces, desynchronization of the boom-bust cycles of coexisting species can lead to the maintenance of high levels of diversity.

evolutionary biology↗

bioRxiv2020

Evolution of diversity in metabolic strategies

Understanding the origin and maintenance of biodiversity is a fundamental problem. Many theoretical approaches have been investigating ecological interactions, such as competition, as potential drivers of diversification. Classical consumer-resource models predict that the number of coexisting species should not exceed the number of distinct resources, a phenomenon known as the competitive exclusion principle. It has recently been argued that including physiological tradeoffs in consumer-resource models can lead to violations of this principle and to ecological coexistence of very high numbers of species. Here we show that these results crucially depend on the functional form of the tradeoff. We investigate the evolutionary dynamics of resource use constrained by tradeoffs and show that if the tradeoffs are non-linear, the system either does not diversify, or diversifies into a number of coexisting species that does not exceed the number of resources. In particular, very high diversity can only be observed for linear tradeoffs.

evolutionary biology↗

bioRxiv2019

The role of multilevel selection in host microbiome evolution

Animals are associated with a microbiome that can affect their reproductive success. It is therefore important to understand how a host and its microbiome coevolve. According to the hologenome concept, hosts and their microbiome form an integrated evolutionary entity, a holobiont, on which selection can potentially act directly. However, this view is controversial and there is an active debate on whether the association between hosts and their microbiomes is strong enough to allow for selection at the holobiont level. Much of this debate is based on verbal arguments, but a quantitative framework is needed to investigate the conditions under which selection can act at the holobiont level. Here we use multilevel selection theory to develop such a framework. We found that selection at the holobiont level can in principle favor a trait that is costly to the microbes but that provides a benefit to the host. However, such scenarios require rather stringent conditions. The degree to which microbiome composition is heritable decays with time, and selection can only act at the holobiont level when this decay is slow enough, which occurs when vertical transmission is stronger than horizontal transmission. Moreover, the host generation time has to be short enough compared to the timescale of the evolutionary dynamics at the microbe level. Our framework thus allows us to quantitatively predict for what kind of systems selection could act at the holobiont level.

evolutionary biology↗

bioRxiv2019

Microbial metabolite fluxes in a model marine anoxic ecosystem

Permanently anoxic regions in the ocean are widespread, and exhibit unique microbial metabolic activity exerting substantial influence on global elemental cycles and climate. Reconstructing microbial metabolic activity rates in these regions has been challenging, due to the technical difficulty of direct rate measurements. In Cariaco Basin, which is the largest permanently anoxic marine basin and an important model system for geobiology, long-term monitoring has yielded time series for the concentrations of biologically important compounds; however the underlying metabolite fluxes remain poorly quantified. Here we present a computational approach for reconstructing vertical fluxes and in situ net production/consumption rates from chemical concentration data, based on a 1-dimensional time-dependent diffusive transport model that includes adaptive penalization of overfitting. We use this approach to estimate spatiotemporally resolved fluxes of oxygen, nitrate, hydrogen sulfide, ammonium, methane and phosphate within the sub-euphotic Cariaco Basin water column (depths 150-900 m, years 2001-2014), and to identify hotspots of microbial chemolithotrophic activity. Predictions of the fitted models are in excellent agreement with the data, and substantially expand our knowledge of the geobiology in Cariaco Basin. In particular, we find that the diffusivity, and consequently fluxes of major reductants such as hydrogen sulfide and methane, are about two orders of magnitude greater than previously estimated, thus resolving a long standing apparent conundrum between electron donor fluxes and measured dark carbon assimilation rates.

ecology↗

bioRxiv2019

Evolutionary dynamics and diversification in changing environments

We use adaptive dynamics models to study how changes in the abiotic environment affect patterns of evolutionary dynamics and diversity in evolving communities of organisms with complex phenotypes. The models are based on the logistic competition model and environmental changes are implemented as a temporal change of the carrying capacity as a function of phenotype. In general we observe that environmental changes cause a reduction in the number of species, in total population size, and in phenotypic diversity. The rate of environmental change is crucial for determining whether a community survives or undergoes extinction. Until some critical rate of environmental changes, species are able to follow evolutionarily the shifting phenotypic optimum of the carrying capacity, and many communities adapt to the changing conditions and converge to new stationary states. When environmental changes stop, such communities gradually restore their initial phenotypic diversity.

biophysics↗

bioRxiv2017

The Cultural Brain Hypothesis: How culture drives brain expansion, underlies sociality, and alters life history

In the last few million years, the hominin brain more than tripled in size. Comparisons across evolutionary lineages suggest that this expansion may be part of a broader trend toward larger, more complex brains in many taxa. Efforts to understand the evolutionary forces driving brain expansion have focused on climatic, ecological, and social factors. Here, building on existing research on learning, we analytically and computationally model the predictions of two closely related hypotheses: The Cultural Brain Hypothesis and the Cumulative Cultural Brain Hypothesis. The Cultural Brain Hypothesis posits that brains have been selected for their ability to store and manage information, acquired through asocial or social learning. The model of the Cultural Brain Hypothesis reveals relationships between brain size, group size, innovation, social learning, mating structures, and the length of the juvenile period that are supported by the existing empirical literature. From this model, we derive a set of predictions--the Cumulative Cultural Brain Hypothesis--for the conditions that favor an autocatalytic take-off characteristic of human evolution. This narrow evolutionary pathway, created by cumulative cultural evolution, may help explain the rapid expansion of human brains and other aspects of our species life history and psychology.

evolutionary biology↗