Ecological scaffolding and the evolution of individuality

Metabolically-driven flows enable exponential growth in macroscopic multicellular yeast

The ecological and evolutionary success of multicellular lineages is due in no small part to their increased size relative to unicellular ancestors. However, large size also poses biophysical challenges, especially regarding the transport of nutrients to all cells; these constraints are typically overcome through multicellular innovations (e.g., a circulatory system). Here we show that an emergent biophysical mechanism - spontaneous fluid flows arising from metabolically-generated density gradients - can alleviate constraints on nutrient transport, enabling exponential growth in nascent multicellular clusters of yeast lacking any multicellular adaptations for nutrient transport or fluid flow. Surprisingly, beyond a threshold size, the metabolic activity of experimentally-evolved snowflake yeast clusters drives large-scale fluid flows that transport nutrients throughout the cluster at speeds comparable to those generated by the cilia of extant multicellular organisms. These flows support exponential growth at macroscopic sizes that theory predicts should be diffusion limited. This work demonstrates how simple physical mechanisms can act as a 'biophysical scaffold' to support the evolution of multicellularity by opening up phenotypic possibilities prior to genetically-encoded innovations. More broadly, our findings highlight how cooption of conserved physical processes is a crucial but underappreciated facet of evolutionary innovation across scales.

Multiscale selection in spatially structured populations

The spatial structure of populations is key to many (eco-)evolutionary processes. In such cases, the strength and sign of selection on a trait may depend on the spatial scale considered. An example is the evolution of altruism: selection in local environments often favours cheaters over altruists, but this can be outweighed by selection at larger scales, favouring clusters of altruists over clusters of cheaters. For populations subdivided into distinct groups, this effect is described formally by multilevel selection theory. However, many populations do not consist of non-overlapping groups but rather (self-)organize into other ecological patterns. We therefore present a mathematical framework for multiscale selection. This framework decomposes natural selection into two parts: local selection, acting within environments of a certain size, and interlocal selection, acting among them. Varying the size of the local environments subsequently allows one to measure the contribution to selection of each spatial scale. To illustrate the use of this framework, we apply it to models of the evolution of altruism and pathogen transmissibility. The analysis identifies how and to what extent ecological processes at different spatial scales contribute to selection and compete, thus providing a rigorous underpinning to eco-evolutionary intuitions.

Neutral diversity in experimental metapopulations

New automated and high-throughput methods allow the manipulation and selection of numerous bacterial populations. In this manuscript we are interested in the neutral diversity patterns that emerge from such a setup in which many bacterial populations are grown in parallel serial transfers, in some cases with population-wide extinction and splitting events. We model bacterial growth by a birth-death process and use the theory of coalescent point processes. We show that there is a dilution factor that optimises the expected amount of neutral diversity for a given number of cycles, and study the power law behaviour of the mutation frequency spectrum for different experimental regimes. We also explore how neutral variation diverges between two recently split populations by establishing a new formula for the expected number of shared and private mutations. Finally, we show the interest of such a setup to select a phenotype of interest that requires multiple mutations.

Characteristic processes of human evolution caused the Anthropocene and may obstruct its global solutions

We propose that the global environmental crises of the Anthropocene are the outcome of a ratcheting process in long-term human evolution which has favoured groups of increased size and greater environmental exploitation. To explore this hypothesis, we review the changes in the human ecological niche. Evidence indicates the growth of the human niche has been facilitated by group-level cultural traits for environmental control. Following this logic, sustaining the biosphere under intense human use will probably require global cultural traits, including legal and technical systems. We investigate the conditions for the evolution of global cultural traits. We estimate that our species does not exhibit adequate population structure to evolve these traits. Our analysis suggests that characteristic patterns of human group-level cultural evolution created the Anthropocene and will work against global collective solutions to the environmental challenges it poses. We illustrate the implications of this theory with alternative evolutionary paths for humanity. We conclude that our species must alter longstanding patterns of cultural evolution to avoid environmental disaster and escalating between-group competition. We propose an applied research and policy programme with the goal of avoiding these outcomes. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.

Evolutionary consequences of nascent multicellular life cycles

A key step in the evolutionary transition to multicellularity is the origin of multicellular groups as biological individuals capable of adaptation. Comparative work, supported by theory, suggests clonal development should facilitate this transition, although this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally reproducing 'snowflake' yeast (Δace2/∆ace2) and aggregative 'floc' yeast (GAL1p::FLO1 /GAL1p::FLO1) with daily selection for rapid growth in liquid media, which favors faster cell division, followed by selection for rapid sedimentation, which favors larger multicellular groups. While both genotypes adapted to this regime, growing faster and having higher survival during the group-selection phase, there was a stark difference in evolutionary dynamics. Aggregative floc yeast obtained nearly all their increased fitness from faster growth, not improved group survival; indicating that selection acted primarily at the level of cells. In contrast, clonal snowflake yeast mainly benefited from higher group-dependent fitness, indicating a shift in the level of Darwinian individuality from cells to groups. Through genome sequencing and mathematical modeling, we show that the genetic bottlenecks in a clonal life cycle also drive much higher rates of genetic drift-a result with complex implications for this evolutionary transition. Our results highlight the central role that early multicellular life cycles play in the process of multicellular adaptation.

Artificial selection of communities drives the emergence of structured interactions

Species-rich communities, such as the microbiota or microbial ecosystems, provide key functions for human health and climatic resilience. Increasing effort is being dedicated to design experimental protocols for selecting community-level functions of interest. These experiments typically involve selection acting on populations of communities, each of which is composed of multiple species. If numerical simulations started to explore the evolutionary dynamics of this complex, multi-scale system, a comprehensive theoretical understanding of the process of artificial selection of communities is still lacking. Here, we propose a general model for the evolutionary dynamics of communities composed of a large number of interacting species, described by disordered generalised Lotka-Volterra equations. Our analytical and numerical results reveal that selection for scalar community functions leads to the emergence, along an evolutionary trajectory, of a low-dimensional structure in an initially featureless interaction matrix. Such structure reflects the combination of the properties of the ancestral community and of the selective pressure. Our analysis determines how the speed of adaptation scales with the system parameters and the abundance distribution of the evolved communities. Artificial selection for larger total abundance is thus shown to drive increased levels of mutualism and interaction diversity. Inference of the interaction matrix is proposed as a method to assess the emergence of structured interactions from experimentally accessible measures.

Evolution: Understanding the origins of facultative multicellular life cycles

Multicellular organisms exhibit a fascinating diversity of life cycles, but little is known about the factors governing life-cycle evolution. New studies of wild yeast and cyanobacteria provide insight into how and why facultative multicellular life cycles arise.

Evolutionarily stable strategy analysis and its links to demography and genetics through invasion fitness

Evolutionarily stable strategy (ESS) analysis pioneered by Maynard Smith and Price took off in part because it often does not require explicit assumptions about the genetics and demography of a population in contrast to population genetic models. Though this simplicity is useful, it obscures the degree to which ESS analysis applies to populations with more realistic genetics and demography: for example, how does ESS analysis handle complexities such as kin selection, group selection and variable environments when phenotypes are affected by multiple genes? In this paper, I review the history of the ESS concept and show how early uncertainty about the method lead to important mathematical theory linking ESS analysis to general population genetic models. I use this theory to emphasize the link between ESS analysis and the concept of invasion fitness. I give examples of how invasion fitness can measure kin selection, group selection and the evolution of linked modifier genes in response to variable environments. The ESSs in these examples depend crucially on demographic and genetic parameters, which highlights how ESS analysis will continue to be an important tool in understanding evolutionary patterns as new models address the increasing abundance of genetic and long-term demographic data in natural populations. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.

Alternating selection for dispersal and multicellularity favors regulated life cycles

The evolution of complex multicellularity opened paths to increased morphological diversity and organizational novelty. This transition involved three processes: cells remained attached to one another to form groups, cells within these groups differentiated to perform different tasks, and the groups evolved new reproductive strategies.1,2,3,4,5 Recent experiments identified selective pressures and mutations that can drive the emergence of simple multicellularity and cell differentiation,6,7,8,9,10,11 but the evolution of life cycles, particularly how simple multicellular forms reproduce, has been understudied. The selective pressure and mechanisms that produced a regular alternation between single cells and multicellular collectives are still unclear.12 To probe the factors regulating simple multicellular life cycles, we examined a collection of wild isolates of the budding yeast S. cerevisiae.12,13 We found that all these strains can exist as multicellular clusters, a phenotype that is controlled by the mating-type locus and strongly influenced by the nutritional environment. Inspired by this variation, we engineered inducible dispersal in a multicellular laboratory strain and demonstrated that a regulated life cycle has an advantage over constitutively single-celled or constitutively multicellular life cycles when the environment alternates between favoring intercellular cooperation (a low sucrose concentration) and dispersal (a patchy environment generated by emulsion). Our results suggest that the separation of mother and daughter cells is under selection in wild isolates and is regulated by their genetic composition and the environments they encounter and that alternating patterns of resource availability may have played a role in the evolution of life cycles.

The role of the ecological scaffold in the origin and maintenance of whole-group trait altruism in microbial populations

BACKGROUND

Kin and multilevel selection provide explanations for the existence of altruism based on traits or processes that enhance the inclusive fitness of an altruist individual. Kin selection is often based on individual-level traits, such as the ability to recognize other altruists, whereas multilevel selection requires a metapopulation structure and dispersal process. These theories are unified by the general principle that altruism can be fixed by positive selection provided the benefit of altruism is preferentially conferred to other altruists. Here we take a different explanatory approach based on the recently proposed concept of an "ecological scaffold". We demonstrate that ecological conditions consisting of a patchy nutrient supply that generates a metapopulation structure, episodic mixing of groups, and severe nutrient limitation, can support or "scaffold" the evolution of altruism in a population of microbes by amplifying drift. This contrasts with recent papers in which the ecological scaffold was shown to support selective processes and demonstrates the power of scaffolding even in the absence of selection.

RESULTS

Using computer simulations motivated by a simple theoretical model, we show that, although an altruistic mutant can be fixed within a single population of non-altruists by drift when nutrients are severely limited, the resulting altruistic population remains vulnerable to non-altruistic mutants. We then show how the imposition of the "ecological scaffold" onto a population of non-altruists alters the balance between selection and drift in a way that supports the fixation and subsequent persistence of altruism despite the possibility of invasion by non-altruists.

CONCLUSIONS

The fixation of an altruistic mutant by drift is possible when supported by ecological conditions that impose a metapopulation structure, episodic mixing of groups, and severe nutrient limitation. This is significant because it offers an alternative explanation for the evolution of altruism based on drift rather than selection. Given the ubiquity of low-nutrient "oligotrophic" environments in which microbes exist (e.g., the open ocean, deep subsurface soils, or under the polar ice caps) our results suggest that altruistic and cooperative behaviors may be highly prevalent among microbial populations.

The effect of bottleneck size on evolution in nested Darwinian populations

Previous work has shown how a minimal ecological structure consisting of patchily distributed resources and recurrent dispersal between patches can scaffold Darwinian properties onto collections of cells. When the timescale of dispersal is long compared with the time to consume resources, patch fitness increases but comes at a cost to cell growth rates. This creates conditions that initiate evolutionary transitions in individuality. A key feature of the scaffold is a bottleneck created during dispersal, causing patches to be founded by single cells. The bottleneck decreases competition within patches and, hence, creates a strong hereditary link at the level of patches. Here, we construct a fully stochastic model to investigate the effect of bottleneck size on the evolutionary dynamics of both cells and collectives. We show that larger bottlenecks simply slow the dynamics, but, at some point, which depends on the parameters of the within-patch model, the direction of evolution towards the equilibrium reverses. Introduction of random fluctuations in bottleneck sizes with some positive probability of smaller sizes counteracts this, even when the probability of smaller bottlenecks is minimal.

Scaffolding individuality: coordination, cooperation, collaboration and community

Processes of evolutionary transition (ET), becoming part of a new reproducing collective while losing the capacity of independent reproduction, seem difficult to track without circularity, since their features-units of selection, individuality, inheritance at multiple levels (MLS1, MLS2)-are products of one process. We describe ET in a non-circular way, noting kinds of interactions among community members necessary for such major transitions that are not instances of those same interactions within community members. Reproducing 'systems' tend to hybridize with environmental components, employing eco-devo scaffolding interactions forming communities. Communities are developmentally scaffolded systems of diverse members engaged in heterogeneous interactions. They may become individuals in their own right with the potential to evolve an inheritance system at the emergent community level. We argue for the explanatory benefits of treating 'individuality' as a special case of 'collectivity'. We characterize an idealized sequence of collective processes-coordination, cooperation and collaboration (3Cs)-which scaffolds transitions to new forms of collective individuality: communities. Hominid evolution and learning draw attention to developmental interactions driving both dimensions of ET: new 'levels of individuality' and inherited 'information systems'. Here, we outline a theoretical perspective that we suggest applies across a wide range of cases and scenarios. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.

Major evolutionary transitions in individuality between humans and AI

That humans might undergo future evolutionary transitions in individuality (ETIs) seems fanciful. However, drawing upon recent thinking concerning the origins of properties that underpin ETIs, I argue that certain ETIs are imminently realizable. Central to my argument is recognition that heritable variance in fitness at higher levels of organization can be externally imposed (scaffolded) by specific ecological structures and cultural practices. While ETIs to eusociality seem highly improbable, ETIs involving symbioses between humans and artificial intelligence (AI) can be readily envisaged. A necessary requirement is that fitness-affecting interactions between humans and AI devices are inherited by offspring. The Mendelian nature of human reproduction ensures that offspring resemble parents. Reproduction of AI devices requires nothing more than transference of algorithms from parental AI devices to devices that are assigned to offspring. This simple copying, combined with societal structures that require humans to carry AI devices, ensures heritable variance in fitness at the level of both interacting partners. Selection at the collective level will drive alignment of replicative fates and increase co-dependency, thus alleviating need for continual imposition of externally imposed scaffolds. I conclude by drawing attention to the immediacy of such transitions and express concern over possibilities for malevolent manipulation. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.

Can models of evolutionary transition clarify the debates over the Neolithic Revolution?

The 'Neolithic Revolution,' sometimes referred to as the emergence of agriculture at its earliest in the southern Levant, is the most significant shift in human history, shaping the world we live in today. Yet, after 100 years of study, its major cause, tempo (gradual or revolutionary), and impact of human intentionality remain disputed. Here, we examine the research potential of an evolutionary transition in individuality (ETI) to clarify this dramatic shift. Applying an ETI research perspective reveals how different causes and conditions lead to the same result, enabling a holistic view rather than a reduction of 'Neolithic' to 'agriculture,' or to one major climatic condition, inheritance system or standard evolutionary model, thus allowing us to clarify and bypass some of these heated, unresolved disputes. Additionally, unlike current archaeological emphasis on 'where,' 'when,' 'why' and 'how' questions, the ETI perspective offers a productive path for resolving a fundamental preliminary anomaly: why and how could the Neolithic lifeway evolve at all, given the selfish interest of individuals in a hunter-gatherer group? We do not intend to solve the shift to Neolithic lifeways, only to offer a fresh lens for examining it, emphasizing the relevance of tracking within and between group differences. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.

Emergent multilevel selection in a simple spatial model of the evolution of altruism

Theories on the evolutionary origins of altruistic behavior have a long history and have become a canonical part of the theory of evolution. Nevertheless, the mechanisms that allow altruism to appear and persist are still incompletely understood. It is well known, however, that the spatial structure of populations is an important determinant. In both theoretical and experimental studies, much attention has been devoted to populations that are subdivided into discrete groups. Such studies typically imposed the structure and dynamics of the groups by hand. Here, we instead present a simple individual-based model in which altruistic organisms spontaneously self-organize into spatially separated colonies that themselves reproduce by binary fission and hence behave as Darwinian entities in their own right. Using software to automatically track the rise and fall of colonies, we are able to apply formal theory on multilevel selection and thus quantify the within- and among-group dynamics. This reveals that individual colonies inevitably succumb to defectors in a within-colony "tragedy of the commons". Even so, altruism persists in the population because more altruistic colonies reproduce more frequently and drive less altruistic ones to extinction. Evidently, the colonies promote the selection of altruism but in turn depend on altruism for their existence; the selection of altruism hence involves a kind of evolutionary bootstrapping. The emergence of the colonies also depends crucially on the length scales of motility, altruism, and competition. This reconfirms the general relevance of these scales for social evolution, but also stresses that their impact can only be understood fully in the light of the emergent eco-evolutionary spatial patterns. The results also suggest that emergent spatial population patterns can function as a starting point for transitions of individuality.

Novel multicellular prokaryote discovered next to an underground stream

A diversity of prokaryotes currently exhibit multicellularity with different generation mechanisms in a variety of contexts of ecology on Earth. In the present study, we report a new type of multicellular bacterium, HS-3, isolated from an underground stream. HS-3 self-organizes its filamentous cells into a layer-structured colony with the properties of a nematic liquid crystal. After maturation, the colony starts to form a semi-closed sphere accommodating clusters of coccobacillus daughter cells and selectively releases them upon contact with water. This is the first report that shows that a liquid-crystal status of cells can support the prokaryotic multicellular behavior. Importantly, the observed behavior of HS-3 suggests that the recurrent intermittent exposure of colonies to water flow in the cave might have been the ecological context that cultivated the evolutionary transition from unicellular to multicellular life. This is the new extant model that underpins theories regarding a role of ecological context in the emergence of multicellularity.

Illuminating a new path to multicellularity

A new species of multicellular bacteria broadens our understanding of prokaryotic multicellularity and provides insight into how multicellular organisms arise.

Tradeoff breaking as model of evolutionary transitions in individuality and the limits of the fitness-decoupling metaphor

Evolutionary transitions in individuality (ETIs) involve the formation of Darwinian collectives from Darwinian particles. The transition from cells to multicellular life is a prime example. During an ETI, collectives become units of selection in their own right. However, the underlying processes are poorly understood. One observation used to identify the completion of an ETI is an increase in collective-level performance accompanied by a decrease in particle-level performance, for example measured by growth rate. This seemingly counterintuitive dynamic has been referred to as fitness decoupling and has been used to interpret both models and experimental data. Extending and unifying results from the literature, we show that fitness of particles and collectives can never decouple because calculations of fitness performed over appropriate and equivalent time intervals are necessarily the same provided the population reaches a stable collective size distribution. By way of solution, we draw attention to the value of mechanistic approaches that emphasise traits, and tradeoffs among traits, as opposed to fitness. This trait-based approach is sufficient to capture dynamics that underpin evolutionary transitions. In addition, drawing upon both experimental and theoretical studies, we show that while early stages of transitions might often involve tradeoffs among particle traits, later—and critical—stages are likely to involve the rupture of such tradeoffs. Thus, when observed in the context of ETIs, tradeoff-breaking events stand as a useful marker of these transitions.

The emergence of group fitness

Whether and how selection can act on collectives rather than single entities has been a tumultuous issue in evolutionary biology for decades. Despite examples of multilevel selection, a simple framework is needed that makes explicit the constraints that lead to the emergence of a "group fitness function." We use evolutionary game theory to show that two constraints are sufficient for the emergence of a well-defined group fitness, which could even apply to multispecies groups. First, different parts of the group contribute to one another's growth via resources produced proportionally to the density of each resource producer (not the density of the population receiving benefits). Second, invading groups do not share these resources with resident groups. Jointly, these two constraints lead to the "entanglement" of invading individuals' outcomes such that individual fitness can no longer be defined and group fitness predicts evolutionary dynamics through the emergence of a higher level evolutionary individual. Group fitness is an emergent property, irreducible to the fitness of the group's parts and exhibiting downward causality on the parts. By formalizing group fitness as a model for evolutionary transitions in individuality, these results open up a broad class of models under the multilevel-selection framework.

Adaptation and phenotypic diversification of Bacillus thuringiensis biofilm are accompanied by fuzzy spreader morphotypes

Bacillus cereus group (Bacillus cereus sensu lato) has a diverse ecology, including various species that produce biofilms on abiotic and biotic surfaces. While genetic and morphological diversification enables the adaptation of multicellular communities, this area remains largely unknown in the Bacillus cereus group. In this work, we dissected the experimental evolution of Bacillus thuringiensis 407 Cry- during continuous recolonization of plastic beads. We observed the evolution of a distinct colony morphotype that we named fuzzy spreader (FS) variant. Most multicellular traits of the FS variant displayed higher competitive ability versus the ancestral strain, suggesting an important role for diversification in the adaptation of B. thuringiensis to the biofilm lifestyle. Further genetic characterization of FS variant revealed the disruption of a guanylyltransferase gene by an insertion sequence (IS) element, which could be similarly observed in the genome of a natural isolate. The evolved FS and the deletion mutant in the guanylyltransferase gene (Bt407ΔrfbM) displayed similarly altered aggregation and hydrophobicity compared to the ancestor strain, suggesting that the adaptation process highly depends on the physical adhesive forces.

Impact of horizontal gene transfer on emergence and stability of cooperative virulence in Salmonella Typhimurium

Intestinal inflammation fuels the transmission of Salmonella Typhimurium (S.Tm). However, a substantial fitness cost is associated with virulence expression. Mutations inactivating transcriptional virulence regulators generate attenuated variants profiting from inflammation without enduring virulence cost. Such variants interfere with the transmission of fully virulent clones. Horizontal transfer of functional regulatory genes (HGT) into attenuated variants could nevertheless favor virulence evolution. To address this hypothesis, we cloned hilD, coding for the master regulator of virulence, into a conjugative plasmid that is highly transferrable during intestinal colonization. The resulting mobile hilD allele allows virulence to emerge from avirulent populations, and to be restored in attenuated mutants competing against virulent clones within-host. However, mutations inactivating the mobile hilD allele quickly arise. The stability of virulence mediated by HGT is strongly limited by its cost, which depends on the hilD expression level, and by the timing of transmission. We conclude that robust evolution of costly virulence expression requires additional selective forces such as narrow population bottlenecks during transmission.

Salmonella Typhimurium virulence is costly and can be lost by mutation during infection. Bakkeren et al. show that virulence restoration via horizontal gene transfer is only transient while transmission bottlenecks promote long-term virulence stability.

Design for an Individual: Connectionist Approaches to the Evolutionary Transitions in Individuality

The truly surprising thing about evolution is not how it makes individuals better adapted to their environment, but how it makes individuals. All individuals are made of parts that used to be individuals themselves, e.g., multicellular organisms from unicellular organisms. In such evolutionary transitions in individuality, the organised structure of relationships between component parts causes them to work together, creating a new organismic entity and a new evolutionary unit on which selection can act. However, the principles of these transitions remain poorly understood. In particular, the process of transition must be explained by “bottom-up” selection, i.e., on the existing lower-level evolutionary units, without presupposing the higher-level evolutionary unit we are trying to explain. In this hypothesis and theory manuscript we address the conditions for evolutionary transitions in individuality by exploiting adaptive principles already known in learning systems. Connectionist learning models, well-studied in neural networks, demonstrate how networks of organised functional relationships between components, sufficient to exhibit information integration and collective action, can be produced via fully-distributed and unsupervised learning principles, i.e., without centralised control or an external teacher. Evolutionary connectionism translates these distributed learning principles into the domain of natural selection, and suggests how relationships among evolutionary units could become adaptively organised by selection from below without presupposing genetic relatedness or selection on collectives. In this manuscript, we address how connectionist models with a particular interaction structure might explain transitions in individuality. We explore the relationship between the interaction structures necessary for (a) evolutionary individuality (where the evolution of the whole is a non-decomposable function of the evolution of the parts), (b) organismic individuality (where the development and behaviour of the whole is a non-decomposable function of the behaviour of component parts) and (c) non-linearly separable functions, familiar in connectionist models (where the output of the network is a non-decomposable function of the inputs). Specifically, we hypothesise that the conditions necessary to evolve a new level of individuality are described by the conditions necessary to learn non-decomposable functions of this type (or deep model induction) familiar in connectionist models of cognition and learning.

The possible modes of microbial reproduction are fundamentally restricted by distribution of mass between parent and offspring

Cells and simple cell colonies reproduce by fragmenting their bodies into pieces. Produced newborns need to grow before they can reproduce again. How big a cell or a cell colony should grow? How many offspring should be produced? Should they be of equal size or diverse? We show that the simple fact that the immediate mass of offspring cannot exceed the mass of parents restricts possible answers to these questions. For example, our theory states that, when mass is conserved in the course of fragmentation, the evolutionarily optimal reproduction mode is fragmentation into exactly two, typically equal, parts. Our theory also shows conditions which promote evolution of asymmetric division or fragmentation into multiple pieces.

Multiple modes of asexual reproduction are observed among microbial organisms in natural populations. These modes are not only subject to evolution, but may drive evolutionary competition directly through their impact on population growth rates. The most prominent transition between two such modes is the one from unicellularity to multicellularity. We present a model of the evolution of reproduction modes, where a parent organism fragments into smaller parts. While the size of an organism at fragmentation, the number of offspring, and their sizes may vary a lot, the combined mass of fragments is limited by the mass of the parent organism. We found that mass conservation can fundamentally limit the number of possible reproduction modes. This has important direct implications for microbial life: For unicellular species, the interplay between cell shape and kinetics of the cell growth implies that the largest and the smallest possible cells should be rod shaped rather than spherical. For primitive multicellular species, these considerations can explain why rosette cell colonies evolved a mechanistically complex binary split reproduction. Finally, we show that the loss of organism mass during sporulation can explain the macroscopic sizes of the formally unicellular microorganism Myxomycetes plasmodium. Our findings demonstrate that a number of seemingly unconnected phenomena observed in unrelated species may be different manifestations of the same underlying process.

OUP accepted manuscript

Temperate phage can initiate lysis or lysogeny after infecting a bacterial host. The genetic switch between lysis and lysogeny is mediated by phage regulatory genes as well as host and environmental factors. Recently, a new class of decision switches was identified in phage of the SPbeta group, mediated by the extracellular release of small, phage-encoded peptides termed arbitrium. Arbitrium peptides can be taken up by bacteria prior to infection, modulating the decision switch in the event of a subsequent phage infection. Increasing the concentration of arbitrium increases the chance that a phage infection will lead to lysogeny, rather than lysis. Although prior work has centered on the molecular mechanisms of arbitrium-induced switching, here we focus on how selective pressures impact the benefits of plasticity in switching responses. In this work, we examine the possible advantages of near-term adaptation of communication-based decision switches used by the SPbeta-like group. We combine a nonlinear population model with a control-theoretic approach to evaluate the relationship between a putative phage reaction norm (i.e. the probability of lysogeny as a function of arbitrium) and the extent of phage reproduction at a near-term time horizon. We measure phage reproduction in terms of a cellular-level metric previously shown to enable comparisons of near-term phage fitness across a continuum from lysis to latency. We show the adaptive potential of communication-based lysis–lysogeny responses and find that optimal switching between lysis and lysogeny increases the near-term phage reproduction compared to fixed responses, further supporting both molecular- and model-based analyses of the putative benefits of this class of decision switches. We further find that plastic responses are robust to the inclusion of cellular-level stochasticity, variation in life history traits, and variation in resource availability. These findings provide further support to explore the long-term evolution of plastic decision systems mediated by extracellular decision-signaling molecules and the feedback between phage reaction norms and ecological context.

Identifying Causes of Social Evolution: Contextual Analysis, the Price Approach, and Multilevel Selection

Kin selection theory and multilevel selection theory are distinct approaches to explaining the evolution of social traits. The latter claims that it is useful to regard selection as a process that can occur on multiple levels of organisation such as the level of individuals and the level of groups. This is reflected in a decomposition of fitness into an individual component and a group component. This multilevel view is central to understanding and characterising evolutionary transitions in individuality, e.g., from unicellular life to multicellular organisms, but currently suffers from the lack of a consistent, quantifiable measure. Specifically, the two major statistical tools to determine the coefficients of such a decomposition, the multilevel Price equation and contextual analysis, are inconsistent and may disagree on whether group selection is present. Here we show that the reason for the discrepancies is that underlying the multilevel Price equation and contextual analysis are two non-equivalent causal models for the generation of individual fitness effects (thus leaving different “remainders” explained by group effects). While the multilevel Price equation assumes that the individual effect of a trait determines an individual's relative success within a group, contextual analysis posits that the individual effect is context-independent. Since these different assumptions reflect claims about the causal structure of the system, the correct approach cannot be determined on general theoretical or statistical grounds but must be identified by experimental intervention. We outline interventions that reveal the underlying causal structure and thus facilitate choosing the appropriate approach. We note that kin selection theory with its focus on the individual is immune to such inconsistency because it does not address causal structure with respect to levels of organisation. In contrast, our analysis of the two approaches to measuring group selection demonstrates that multilevel selection theory adds meaningful (falsifiable) causal structure to explain the sources of individual fitness and thereby constitutes a proper refinement of kin selection theory. Taking such refined causal structure into account seems indispensable for studying evolutionary transitions in individuality because these transitions are characterised by changes in the selection pressures that act on the respective levels.

On the evolutionary origins of host-microbe associations

Many microorganisms with high prevalence in host populations are beneficial to the host and maintained by specialized transmission mechanisms. Although microbial promotion of host fitness and specificity of the associations undoubtedly enhance microbial prevalence, it is an open question whether these symbiotic traits are also a prerequisite for the evolutionary origin of prevalent microbial taxa. To address this issue, we investigate how processes without positive microbial effects on host fitness or host choice can influence the prevalence of certain microbes in a host population. Specifically, we develop a theoretical model to assess the conditions under which particular microbes can become enriched in animal hosts even when they are not providing a specific benefit to a particular host. We find increased prevalence of specific microbes in a host when both show some overlap in their lifecycles, and especially when both share dispersal routes across a patchy habitat distribution. Our results emphasize that host enrichment per se is not a reliable indicator of beneficial host-microbe interactions. The resulting increase in time spent associated with a host may nevertheless give rise to new selection conditions, which can favor microbial adaptations toward a host-associated lifestyle, and, thus, it could be the foundation for subsequent evolution of mutually beneficial coevolved symbioses.

The evolution of convex trade-offs enables the transition towards multicellularity

The evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade-off between survival and reproduction. However, this has never been tested and these transitions remain poorly understood at the ecological and genetic level. Here, we study the evolution of cell groups in ten isogenic lines of the unicellular green algae Chlamydomonas reinhardtii with prolonged exposure to a rotifer predator. We confirm that growth in cell groups is heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolve in all cell group isolates; these are linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

Multicellularity is a major evolutionary transition that remains poorly characterized at the ecological and genetic level. Exposing unicellular green algae to a rotifer predator showed that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.

Cryptic surface-associated multicellularity emerges through cell adhesion and its regulation

The repeated evolution of multicellularity led to a wide diversity of organisms, many of which are sessile, including land plants, many fungi, and colonial animals. Sessile organisms adhere to a surface for most of their lives, where they grow and compete for space. Despite the prevalence of surface-associated multicellularity, little is known about its evolutionary origin. Here, we introduce a novel theoretical approach, based on spatial lineage tracking of cells, to study this origin. We show that multicellularity can rapidly evolve from two widespread cellular properties: cell adhesion and the regulatory control of adhesion. By evolving adhesion, cells attach to a surface, where they spontaneously give rise to primitive cell collectives that differ in size, life span, and mode of propagation. Selection in favor of large collectives increases the fraction of adhesive cells until a surface becomes fully occupied. Through kin recognition, collectives then evolve a central-peripheral polarity in cell adhesion that supports a division of labor between cells and profoundly impacts growth. Despite this spatial organization, nascent collectives remain cryptic, lack well-defined boundaries, and would require experimental lineage tracking technologies for their identification. Our results suggest that cryptic multicellularity could readily evolve and originate well before multicellular individuals become morphologically evident.

The Consequences of Budding versus Binary Fission on Adaptation and Aging in Primitive Multicellularity

Early multicellular organisms must gain adaptations to outcompete their unicellular ancestors, as well as other multicellular lineages. The tempo and mode of multicellular adaptation is influenced by many factors including the traits of individual cells. We consider how a fundamental aspect of cells, whether they reproduce via binary fission or budding, can affect the rate of adaptation in primitive multicellularity. We use mathematical models to study the spread of beneficial, growth rate mutations in unicellular populations and populations of multicellular filaments reproducing via binary fission or budding. Comparing populations once they reach carrying capacity, we find that the spread of mutations in multicellular budding populations is qualitatively distinct from the other populations and in general slower. Since budding and binary fission distribute age-accumulated damage differently, we consider the effects of cellular senescence. When growth rate decreases with cell age, we find that beneficial mutations can spread significantly faster in a multicellular budding population than its corresponding unicellular population or a population reproducing via binary fission. Our results demonstrate that basic aspects of the cell cycle can give rise to different rates of adaptation in multicellular organisms.

Aggregative cycles evolve as a solution to conflicts in social investment

Multicellular organization is particularly vulnerable to conflicts between different cell types when the body forms from initially isolated cells, as in aggregative multicellular microbes. Like other functions of the multicellular phase, coordinated collective movement can be undermined by conflicts between cells that spend energy in fuelling motion and ‘cheaters’ that get carried along. The evolutionary stability of collective behaviours against such conflicts is typically addressed in populations that undergo extrinsically imposed phases of aggregation and dispersal. Here, via a shift in perspective, we propose that aggregative multicellular cycles may have emerged as a way to temporally compartmentalize social conflicts. Through an eco-evolutionary mathematical model that accounts for individual and collective strategies of resource acquisition, we address regimes where different motility types coexist. Particularly interesting is the oscillatory regime that, similarly to life cycles of aggregative multicellular organisms, alternates on the timescale of several cell generations phases of prevalent solitary living and starvation-triggered aggregation. Crucially, such self-organized oscillations emerge as a result of evolution of cell traits associated to conflict escalation within multicellular aggregates.

In aggregative multicellular life cycles, cells come together in heterogenous aggregates, whose collective function benefits all the constituent cells. Current explanations for the evolutionary stability of such organization presume that alternating phases of aggregation and dispersal are already in place. Here we propose that, instead of being externally driven, the temporal arrangement of aggregative life cycles may emerge from the interplay between ecology and evolution in populations with differential motility. In our model, cell motility underpins group formation and allows cells to forage individually and collectively. Notably, slower cells can exploit the propulsion by faster cells within multicellular groups. When the level of such exploitation is let evolve, increasing social conflicts are associated to the evolutionary emergence of self-sustained oscillations. Akin to aggregative life cycles, resource exhaustion triggers group formation, whereas conflicts within multicellular groups restrain resource consumption, thus paving the way for the subsequent unicellular phase. The evolutionary transition from equilibrium coexistence to life cycles solves conflicts among heterogenous cell types by integrating them on a timescale longer than cell division, that comes to be associated to multicellular organization.

Evolution of Cellular Differentiation: From Hypotheses to Models

Cellular differentiation is one of the hallmarks of complex multicellularity, allowing individual organisms to capitalize on among-cell functional diversity. The evolution of multicellularity is a major evolutionary transition that allowed for the increase of organismal complexity in multiple lineages, a process that relies on the functional integration of cell-types within an individual. Multiple hypotheses have been proposed to explain the origins of cellular differentiation, but we lack a general understanding of what makes one cell-type distinct from others, and how such differentiation arises. Here, we describe how the use of Boolean networks (BNs) can aid in placing empirical findings into a coherent conceptual framework, and we emphasize some of the standing problems when interpreting data and model behaviors.

Germ lines and extended selection during the evolutionary transition to multicellularity

The major evolutionary transitions from unicellular organisms to multicellularity resulted in a profusion of complex life forms. During the transition from single cells to multicellular life, groups of cells acquired the capacity for reproduction as discrete units; however, the selective causes and underlying mechanisms remain debated. One perspective views the evolution of multicellularity as a shift in the timescale at which natural selection primarily operates-from that of individual cells to the timescale of reproducing groups of cells. Therefore, a distinguishing feature of multicellular reproduction, as opposed to simple growth of a multicellular collective, is that the capacity for reproduction must develop over a timescale that is greater than the reproductive timescale of a single cell. Here, I suggest that the emergence of specialized reproductive cells (the germ line) was an essential first stage of the evolutionary transition to multicellularity because it imposed the necessary "delay"-allowing natural selection to operate over the longer timescale of a multicellular life cycle, ultimately resulting in the evolution of complex multicellular organisms. This perspective highlights the possibility that the ubiquity of a germ-soma distinction among complex multicellular organisms reflects the fact that such life cycles, on first emergence, had the greatest propensity to participate in Darwinian evolution.

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity

Interactions among microbial cells can generate new chemistries and functions, but exploitation requires establishment of communities that reliably recapitulate community-level phenotypes. Using mechanistic mathematical models, we show how simple manipulations to population structure can exogenously impose Darwinian-like properties on communities. Such scaffolding causes communities to participate directly in the process of evolution by natural selection and drives the evolution of cell-level interactions to the point where, despite underlying stochasticity, derived communities give rise to offspring communities that faithfully re-establish parental phenotype. The mechanism is akin to a developmental process (developmental correction) that arises from density-dependent interactions among cells. Knowledge of ecological factors affecting evolution of developmental correction has implications for understanding the evolutionary origin of major egalitarian transitions, symbioses, and for top-down engineering of microbial communities.

Toward a dynamical understanding of microbial communities

The challenge of moving beyond descriptions of microbial community composition to the point where understanding underlying eco-evolutionary dynamics emerges is daunting. While it is tempting to simplify through use of model communities composed of a small number of types, there is a risk that such strategies fail to capture processes that might be specific and intrinsic to complexity of the community itself. Here, we describe approaches that embrace this complexity and show that, in combination with metagenomic strategies, dynamical insight is increasingly possible. Arising from these studies is mounting evidence of rapid eco-evolutionary change among lineages and a sense that processes, particularly those mediated by horizontal gene transfer, not only are integral to system function, but are central to long-term persistence. That such dynamic, systems-level insight is now possible, means that the study and manipulation of microbial communities can move to new levels of inquiry. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Personality neuroscience and psychopathology: should we start with biology and look for neural-level factors?

"Personality is an abstraction used to explain consistency and coherency in an individual's pattern of affects, cognitions, desires and behaviors [ABCDs]" (Revelle, 2007, p. 37). But personality research currently provides more a taxonomy of patterns than theories of fundamental causes. Psychiatric disorders can be viewed as involving extremes of personality but are diagnosed via symptom patterns not biological causes. Such surface-level taxonomic description is necessary for science, but consistent predictive explanation requires causal theory. Personality constructs, and especially their clinical extremes, should predict variation in ABCD patterns, with parsimony requiring the lowest effective causal level of explanation. But, even biologically inspired personality theories currently use an intuitive language-based approach for scale development that lacks biological anchors. I argue that teleonomic "purpose" explains the organisation and outputs of conserved brain emotion systems, where high activation is adaptive in specific situations but is otherwise maladaptive. Simple modulators of whole-system sensitivity evolved because the requisite adaptive level can vary across people and time. Sensitivity to a modulator is an abstract predictive personality factor that operates at the neural level but provides a causal explanation of both coherence and occasional apparent incoherence in ABCD variation. Neuromodulators impact all levels of the "personality hierarchy" from metatraits to aspects: stability appears altered by serotonergic drugs, neuroticism by ketamine and trait anxiety by simple anxiolytic drugs. Here, the tools of psychiatry transfer to personality research and imply both interaction between levels and oblique factor mappings to ABCD. On this view, much psychopathology reflects extremes of neural-level personality factors, and we can view much pharmacotherapy as temporarily altering personality. So, particularly for personality factors linked to basic emotions and their disorders, I think we should start with evolutionary biology and look directly at conserved neural-level modulators for our explanatory personality constructs and only invoke higher order, emergent, explanations when neural-level explanation fails.

Experimental manipulation of selfish genetic elements links genes to microbial community function

Microbial communities underpin the Earth's biological and geochemical processes, but their complexity hampers understanding. Motivated by the challenge of diversity and the need to forge ways of capturing dynamical behaviour connecting genes to function, biologically independent experimental communities comprising hundreds of microbial genera were established from garden compost and propagated on nitrogen-limited minimal medium with cellulose (paper) as sole carbon source. After 1 year of bi-weekly transfer, communities retained hundreds of genera. To connect genes to function, we used a simple experimental manipulation that involved the periodic collection of selfish genetic elements (SGEs) from separate communities, followed by pooling and redistribution across communities. The treatment was predicted to promote amplification and dissemination of SGEs and thus horizontal gene transfer. Confirmation came from comparative metagenomics, which showed the substantive movement of ecologically significant genes whose dynamic across space and time could be followed. Enrichment of genes implicated in nitrogen metabolism, and particularly ammonification, prompted biochemical assays that revealed a measurable impact on community function. Our simple experimental strategy offers a conceptually new approach for unravelling dynamical processes affecting microbial community function.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.

Coexistence and cooperation in structured habitats

Background

Natural habitats are typically structured, imposing constraints on inhabiting populations and their interactions. Which conditions are important for coexistence of diverse communities, and how cooperative interaction stabilizes in such populations, have been important ecological and evolutionary questions.

Results

We investigate a minimal ecological framework of microbial population dynamics that exhibits crucial features to show coexistence: Populations repeatedly undergo cycles of separation into compartmentalized habitats and mixing with new resources. The characteristic time-scale is longer than that typical of individual growth. Using analytic approximations, averaging techniques and phase-plane methods of dynamical systems, we provide a framework for analyzing various types of microbial interactions. Population composition and population size are both dynamic variables of the model; they are found to be decoupled both in terms of time-scale and parameter dependence. We present specific results for two examples of cooperative interaction by public goods: collective antibiotics resistance, and enhanced iron-availability by pyoverdine. We find stable coexistence to be a likely outcome.

Conclusions

The two simple features of a long mixing time-scale and spatial compartmentalization are enough to enable coexisting strains. In particular, costly social traits are often stabilized in such an environment—and thus cooperation established.