Biology subjects

Libby, E.

Publications and source records attributed to Libby, E..

At least 19 recordsLinked to original sources

bioRxiv2026

From cooperation to predation: the evolutionary origins of phagocytosis

A major transition in the evolution of eukaryotic cells was phagocytosis: the ability of one cell to engulf another. In some cases, the engulfed cell persists, forming an endosymbiosis which is often mutually beneficial. However, it is unclear whether the interaction between the ancestors was also cooperative. There are clear benefits to developing the ability to eat a competitor, but can it ever be beneficial to eat a cooperator? We use a dynamical systems framework to identify the ecological conditions under which phagocytosis can evolve from a system of cooperating microbes.Beginning with a system of two cooperating species, we use invasion analysis to identify the parameter regimes under which a phagocytosing mutant can invade and the subsequent population dynamics. We identify a critical threshold that determines whether an invading predator will coexist with the cooperative community or replace members. Repeatedly invading with different predators, we find that the system saturates when there are three coexisting species, though this community does not have a single optimal composition. However, if we incorporate additional costs, we find there is a single evolutionarily stable community of two cooperators and a pure predator. Ultimately, we show that it is possible for phagocytosis to evolve from a cooperative community and, moreover, coexist with the original cooperating species.

evolutionary biology↗

bioRxiv2026

Obligate multicellularity circumvents population genetic barriers to collective-level adaptation

Complex multicellularity has evolved in just five lineages (animals, plants, brown algae, red algae, and fungi) and in each case, these organisms develop clonally and are obligately multicellular. While prior work has shown that clonal development plays a critical role in the evolution of complex multicellularity, none has disentangled this from the impact of obligate vs facultative multicellular life cycles. Here we use experimental evolution with engineered snowflake yeast (Saccharomyces cerevisiae) to directly test how life cycle structure affects multicellular adaptation. We created isogenic strains capable of switching between unicellular and clonal multicellular phases, then evolved populations for 192 days under obligately multicellular, facultatively multicellular, and obligately unicellular regimes. Obligately multicellular populations rapidly evolved larger size, primarily driven by a whole genome duplication, in all five replicates. Facultative populations showed dramatically constrained evolution, with tetraploidy evolving in only 2/10 facultative populations despite experiments demonstrating that it is strongly beneficial across the full life cycle. Mathematical modeling reveals the mechanistic basis for this constraint: facultative life cycles create establishment barriers through two population genetic effects. Group formation dramatically reduces the number of units of selection, making beneficial multicellular mutations vulnerable to drift. This asymmetry in population size between life cycle phases also allows cell-level selection to overpower group-level selection, eliminating mutations that provide group-level benefits but carry cell-level costs. These findings demonstrate that obligate multicellularity circumvents fundamental population genetic barriers to collective-level adaptation, helping explain why complex multicellularity has evolved exclusively in obligately multicellular lineages, and suggesting similar constraints may operate in other evolutionary transitions in individuality.

evolutionary biology↗

bioRxiv2026

The limits of information in precise regulation of early multicellular life cycles

A key step in the evolution of complex multicellularity is the emergence of regulated life cycles that coordinate growth and reproduction. One potential route toward regulation involves co-opting intrinsic information: cues generated by routine cellular activities such as aging or mechanical stress from growth. Here, we model the simplest form of multicellular organization, linear filaments, to investigate whether intrinsic information can be harnessed to produce regular multicellular life cycles. Based on our analyses, we find that these information sources face an inherent trade-off between flexibility and regularity. Some sources, such as mechanical stress, precisely regulate when reproduction occurs but generate only a single reproductive mode. Others, such as cell age, can in principle produce diverse life cycles but fail to generate any of them reliably. Combining information sources through simple genetic circuits reduces variance in some cases, but the range of achievable life cycles remains constrained. Together these results suggest that while intrinsic information may facilitate early multicellular evolution, there are significant limitations on the degree to which it can be harnessed to evolve tightly-regulated, flexible life cycles. Our work highlights the constraints faced by nascent multicellular organisms and the evolutionary innovations likely required for coordinated multicellular development.

evolutionary biology↗

bioRxiv2025

The fitness costs of reproductive specialization scale inversely with organismal size

The evolution of reproductive specialization represents a fundamental innovation in multicellular life, yet the conditions favoring its evolution remain poorly understood. Here, we develop a population genetic framework that examines the fitness cost of reproductive specialization as a function of organism size. We show analytically that the costs of specialization decrease dramatically with organism size. For example, while a 4-cell organism with 50% somatic cells experiences a 50% reduction in population-level exponential growth rate (the same as the two-fold cost of sex), a hundred-cell organism faces only a 15% reduction, a thousand-cell organism 10%, a million-cell organism 5%, and a billion-cell organism merely 3.3%. This scaling relationship arises from the fact that proportionally more cellular growth in larger organisms is required for development, reducing the rate at which the fitness costs of specialization are compounded over multicellular generations. We contextualize our mathematical model with data from the volvocine green algae, showing that simple theoretical predictions closely match empirical measurements. While cellular differentiation demands that somatic advantages compensate for lost reproductive potential, we demonstrate that these compensatory requirements diminish with the logarithm of organism size, fundamentally altering the cost-benefit landscape for large organisms and potentially driving the evolution of a size-differentiation ratchet. This size-scaling relationship helps explain the broad association between large organismal size and multicellular complexity.

evolutionary biology↗

bioRxiv2025

Endosymbiosis: metabolic trade-offs drive reproductive synchronization

Endosymbiotic relationships have fueled the evolution of complex life. The persistence of these relationships relies on coordinating the reproduction of hosts and their guests. Yet, such coordination may come at a cost, as one or both partners may need to slow their growth to synchronize. Here, we examine the fitness consequences of synchronization by using a combination of mathematical and bacterial metabolic models. Analyzing millions of putative host-guest pairings, we find that synchronization is typically costly for hosts but beneficial for guests. We show that synchronization can occur when hosts relinquish metabolic resources to guests. Given the costs to hosts, we investigate whether hosts can benefit from growing faster, at the risk of losing their endosymbionts. Our mathematical model suggests this outcome is theoretically possible, but metabolic modeling consistently indicates that synchronization increases overall fitness-- provided the formation of new endosymbioses is rare. When new relationships can readily form, the optimal strategy shifts: hosts maximize fitness by growing as fast as possible, leading to regular cycles of loss and reacquisition of their guests. Overall, our findings indicate that while synchronization is costly for hosts, it offers long-term fitness benefits in contexts where endosymbionts are not easily replaced.

evolutionary biology↗

bioRxiv2025

Forecasting multi-trait resistance evolution under antibiotic stress

Many bacteria rely on efflux pumps to survive antibiotic stress, and exposure to antibiotics often leads to mutations in pump genes or their regulators that increase pump expression. Predicting the spectrum of these mutations is important for designing effective antibiotic treatments, but the underlying regulatory networks are large and complex, making them difficult to map experimentally. To address this challenge, we developed a mathematical framework that integrates dynamical equations for efflux pump regulation with a genetic algorithm for parameter estimation and evolutionary simulations. Using this framework, we simulated in silico evolution of Pseudomonas aeruginosa under exposure to the antibiotics meropenem, tobramycin, and ciprofloxacin. The simulations revealed mutational spectra affecting the expression of four RND efflux pumps and their shared regulatory network. The most frequently mutated genes were single-target regulators that matched well with previous observations in clinical and in vitro studies. The model also showed that the shared use of the OprM protein by two pumps is a key factor shaping their distinct mutational patterns. Mutations often produced multi-trait phenotypes, manifesting as collateral sensitivity or cross-resistance to antibiotics not used for selection. While cross-resistance evolved readily, its extent depended on initial pump expression levels and thus may vary between strains. Finally, simulations of changing environments showed that efflux pump genes tend to be lost in the absence of antibiotics, suggesting a potential strategy to steer bacterial evolution toward reduced capacity to re-evolve resistance.

microbiology↗

bioRxiv2025

The dynamics of thermal stress events determine whether thermotolerant endosymbionts improve or hamper survival of coral reefs

Coral reefs are increasingly threatened by marine heatwaves which can cause devastating coral bleaching events. Despite this, corals can sometimes survive often altering their symbiont composition toward more thermally-tolerant taxa in response to thermal stress. The long-term efficacy of such a strategy remains poorly understood, in particular, the function of bleaching as an acclimation agent. Here, we use a model of coral-symbiont dynamics, which includes novel and empirically intractable aspects of symbiont thermal tolerance, to investigate how changes in coral endosymbiont composition influence reef survival under differing patterns of heat stress. We find that thermal stress-induced bleaching can act as an acclimation mechanism, but its effectiveness is modulated by the interplay between thermal stress intensity and frequency. When thermal stress remains moderate in frequency and intensity, acclimation can occur as longer intervals between stress events promote post-bleaching coral recovery via a beneficial sequence of hosting thermally-tolerant then thermally-sensitive symbionts, interspersing thermal resilience with periods of faster coral growth. In contrast, when thermal stress intensity increases rapidly and occurs at higher frequency, sustained dominance of thermally-tolerant symbionts is favoured, providing a temporary survival strategy that delays reef collapse but with the trade-off of lower coral growth. While in this latter scenario, acclimation may be less effective due to disrupted reef population structure, it does provide a mechanism for corals to "buy time", during which other adaptive processes may occur enabling longer-term coral survival. However, under a real-world low emission IPCC future scenario, even this flexible survival strategy may still lead to an immediate and sustained fall in coral cover. By capturing both, 1) thermal frequency and intensity dynamics, along with, 2) symbiont thermotolerance preferences and linked growth trade-offs we provide a coral survival model which can be used as a tool to inform strategic coral reef management frameworks promoting reef resilience.

ecology↗

bioRxiv2025

A Multi-Tetracycline Responsive Induction System for Gene Expression in Bacillus subtilis

Well-characterized induction systems that offer tightly regulated, graded, and homogeneous control of gene expression are essential tools for basic and applied microbiology. Tetracycline- based induction systems are widely used non-toxic expression systems in bacteria, however the GRAS and industrially relevant model organism Bacillus subtilis currently lacks a tightly regulated, sensitive system that is robust to media and growth conditions. Here we adapted features of existing tetracycline induction systems to the specific requirements of B. subtilis by engineering a codon-optimized TetR repressor, enhanced promoter and operator architecture, and a modular shuttle vector enabling stable, single-copy chromosomal integration. The resulting system achieves [~]1000-fold dynamic range with minimal leakiness, using subinhibitory concentrations of anhydrotetracycline, chlortetracycline, and doxycycline as inducers in rich and minimal media as well as in colonies. We further quantify the titration parameters and non-inhibitory ranges for each inducer and growth condition, providing a well-characterized and versatile tool for inducible gene expression in B. subtilis. ImportanceBacillus subtilis is an important bacterial model organism with applications in biotechnology and industrial microbiology. However, tools for tightly controlled gene regulation that are robust to growth conditions remain limited. We developed a tetracycline-inducible system tailored to B. subtilis, providing strong, tunable expression with minimal leaky expression across diverse growth conditions. Due to its enhanced sensitivity, tight regulation, and homogeneous induction of the bacterial population, it enables precision titration of gene expression for a variety of downstream applications such as physiology studies, pathway optimization, biotechnology, and colony-based screening.

microbiology↗

bioRxiv2024

Ecological resource competition as a driver of metallome evolution

The oldest nitrogenase isozyme, emerging a billion years or more before the Great Oxidation Event (GOE), required a molybdenum (Mo)-based cofactor. "Alternative" nitrogenases using iron (Fe) or vanadium (V) cofactors evolved only after the GOE. This history is puzzling because environmental Fe availability decreased after the GOE, while Mo availability increased, due to the contrasting environmental redox behaviors of these elements. Why, then, did the alternatives emerge only after the GOE? Using a model constrained by known microbial Mo quotas, we demonstrate that a strong selection pressure for the use of metals in nitrogenase other than Mo is a plausible consequence of competition between nitrogen-fixing prokaryotes and nitrate-reducing microbes, which require Mo for nitrate reduction and assimilation. This competition would have intensified after the GOE due to increasing availability of nitrate, explaining the evolutionary timing of nitrogenases isozymes. Ecological resource competition therefore emerges as a third driver of metallome evolution in deep-time, alongside the relative environmental availabilities and adaptive advantages of particular metals.

evolutionary biology↗

bioRxiv2024

Competition and cooperation: The plasticity of bacteria interactions across environments

Bacteria live in diverse communities, forming complex networks of interacting species. A central question in bacterial ecology is why some species engage in cooperative interactions, whereas others compete. But this question often neglects the role of the environment. Here, we use genome-scale metabolic networks from two different open-access collections (AGORA and CarveMe) to assess pairwise interactions of different microbes in varying environmental conditions (provision of different environmental compounds). By scanning thousands of environments for 10,000 pairs of bacteria from each collection, we found that most pairs were able to both compete and cooperate depending on the availability of environmental resources. This approach allowed us to determine commonalities between environments that could facilitate the potential for cooperation or competition between a pair of species. Namely, cooperative interactions, especially obligate, were most common in less diverse environments. Further, as compounds were removed from the environment, we found interactions tended to degrade towards obligacy. However, we also found that on average at least one compound could be removed from an environment to switch the interaction from competition to facultative cooperation or vice versa. Together our approach indicates a high degree of plasticity in microbial interactions to the availability of environmental resources.

microbiology↗

bioRxiv2024

Adaptive evolutionary trajectories in complexity: repeated transitions between unicellularity and differentiated multicellularity

Multicellularity spans a wide gamut in terms of complexity, from simple clonal clusters of cells to large-scale organisms composed of differentiated cells and tissues. While recent experiments have demonstrated that simple forms of multicellularity can readily evolve in response to different selective pressures, it is unknown if continued exposure to those same selective pressures will result in the evolution of increased multicellular complexity. We use mathematical models to consider the adaptive trajectories of unicellular organisms exposed to periodic bouts of abiotic stress, such as drought or antibiotics. Populations can improve survival in response to the stress by evolving multicellularity or cell differentiation--or both; however, these responses have associated costs when the stress is absent. We define a parameter space of fitness-relevant traits and identify where multicellularity, differentiation, or their combination is fittest. We then study the effects of adaptation by allowing populations to fix mutations that improve their fitness. We find that while the same mutation can be beneficial to phenotypes with different complexity, e.g. unicellularity and differentiated multicellularity, the magnitudes of their effects can differ and alter which phenotype is fittest. As a result, we observe adaptive trajectories that gain and lose complexity. We also show that the order of mutations, historical contingency, can cause some transitions to be permanent in the absence of neutral evolution. Ultimately, we find that continued exposure to a selective driver for multicellularity can either lead to increasing complexity or a return to unicellularity.

evolutionary biology↗

bioRxiv2023

Division of labor promotes the entrenchment of multicellularity

Simple multicellularity evolves readily in diverse unicellular species, but nascent multicellular groups are prone to reversion to unicellularity. Successful transitions to multicellularity therefore require subsequent mutations that promote the entrenchment of the higher-level unit, stabilizing it through time. Here we explore the causes of entrenchment using digital evolution. When faced with a trade-off between cellular metabolic productivity and information fidelity, digital "multicells" often evolve reproductive division of labor. Because digital "unicells" cannot circumvent this trade-off, unicellular revertants tend to exhibit low fitness relative to their differentiated multicellular ancestors. Thus, division of labor can drive the entrenchment of multicellularity. More generally, division of labor may play a crucial role in major transitions, enriching the complexity and functionality of higher-level units while enhancing their evolutionary stability.

evolutionary biology↗

bioRxiv2023

Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment

The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earths ecosystems. Yet little is known about how early steps in the evolution of multicellularity transform eco-evolutionary dynamics, e.g., via niche expansion processes that may facilitate coexistence. Using long-term experimental evolution in the snowflake yeast model system, we show that the evolution of multicellularity drove niche partitioning and the adaptive divergence of two distinct, specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subject to selection for rapid growth in rich media, followed by selection favoring larger group size. Both small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations. These small and large sized snowflake yeast lineages specialized on divergent aspects of a trade-off between growth rate and survival, mirroring predictions from ecological theory. Through modeling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically-impactful emergent properties of this evolutionary transition.

evolutionary biology↗

bioRxiv2022

Minor variations in multicellular life cycles have major effects on adaptation

Multicellularity has evolved several independent times over the past hundreds of millions of years and given rise to a wide diversity of complex life. Recent studies have found that large differences in the fundamental structure of early multicellular life cycles can affect fitness and influence multicellular adaptation. Yet, there is an underlying assumption that at some scale or categorization multicellular life cycles are similar in terms of their adaptive potential. Here, we consider this possibility by exploring adaptation in a class of simple multicellular life cycles of filamentous organisms that only differ in one respect, how many daughter filaments are produced. We use mathematical models and evolutionary simulations to show that despite the similarities, qualitatively different mutations fix. In particular, we find that mutations with a tradeoff between cell growth and group survival, i.e. "selfish" or "altruistic" traits, spread differently. Specifically, altruistic mutations more readily spread in life cycles that produce few daughters while in life cycles producing many daughters either type of mutation can spread depending on the environment. Our results show that subtle changes in multicellular life cycles can fundamentally alter adaptation. Author summaryEarly forms of multicellular organisms exhibit a wide range of life cycles. Though studies have explored how the structure of a life cycle determines the fitness of early multicellular organisms, far less is known about how it affects their adaptation. Studies that do investigate adaptation typically focus on large scale differences between life cycles, implicitly assuming that at some scale life cycles are similar in terms of their adaptation. In this study we consider this assumption by analyzing adaptation in a class of early multicellular life cycles where the only difference between them is the number of offspring they produce. We use mathematical models and evolutionary simulations to compute the fate of mutations that are either altruistic or selfish, depending on their effects on single cells and the groups to which they belong. We find that despite the similarity between life cycles they can adapt very differently. In particular, life cycles that produce few offspring consistently adapt via altruistic traits, while life cycles that produce many offspring adapt via either altruistic or selfish traits depending on the environment. Ultimately, we find that small scale differences in multicellular life cycles can have large effects on adaptation.

evolutionary biology↗

bioRxiv2022

Overexpression of the plastidal pseudo-protease AtFtsHi3 confers drought tolerance without penalizing growth

Drought is one of the most severe environmental stresses affecting plant biomass production and quality, however, the molecular mechanisms of drought response in plants remain unclear. Here, we demonstrate that overexpression of the Arabidopsis gene FTSHi3 under the influence of its endogenous, or the 35S constitutive promoter results in drought-tolerant phenotypes without penalising plant growth. FTSHi3 encodes a pseudo-protease located in the chloroplast envelope and knock-down mutants (ftshi3-1) have previously been found to be drought tolerant, but highly reduced in growth. Changes in FtsHi3 transcript abundance therefore seems to induce drought tolerance in Arabidopsis thaliana. Overexpression of FTSHi3 (pFTSHi3-OE) impacts leaf stomatal density, lowers stomatal conductance and increases water use efficiency. To explore the underlying mechanisms behind this, we compared the proteomes of ftshi3-1 and pFTSHi3-OE to wild type plants grown under drought and watered conditions. Under drought conditions, the drought related processes osmotic stress, water transport and response to abscisic acid were enriched, indicating that pFtsHi3-OE and ftshi3-1 mutants are more active in their response to drought than the wild-type. The proteins HSP90, HSP93 and TIC110 were more abundant in the knock-down mutant, which suggests that FtsHi3 might play a downstream role in chloroplast pre-protein import. Increased abundance of FtsH7/9 and FtsH11, FtsH12 and FtsHi4 in ftshi3-1 combined with the fact that FtsH proteases function as homo- or heteromeric complexes suggests that these proteases may be possible interacting partners. To explore this, we constructed mathematical models that show FtsHi3 likely interacts with at least two other (pseudo-) proteases.

biochemistry↗

bioRxiv2022

Clonal development, not aggregation, drives the transition to multicellularity in an isogenic model system

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, though this hypothesis has never been tested in a single model system. We evolved 20 replicate populations of otherwise isogenic clonally-reproducing snowflake yeast ({Delta}ace2/{Delta}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 of 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 biological 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.

evolutionary biology↗

bioRxiv2022

Metabolic compatibility and the rarity of prokaryote endosymbioses

The evolution of the mitochondria was a significant event that gave rise to the eukaryotic lineage and most large complex life. Central to the origins of the mitochondria was an endosymbiosis between prokaryotes. Yet, despite the potential benefits that can stem from a prokaryotic endosymbiosis, their modern occurrence is exceptionally rare. While many factors may contribute to their rarity, we lack methods for estimating the extent to which they constrain the appearance of a prokaryotic endosymbiosis. Here, we address this knowledge gap by examining the role of metabolic compatibility between a prokaryotic host and endosymbiont. We use genome-scale metabolic models from three different databases (AGORA, KBase, and CarveMe) to assess the viability, fitness, and adaptability of potential prokaryotic endosymbioses. We find that while more than half of host-endosymbiont pairings are metabolically viable, the resulting endosymbioses have reduced growth rates compared to their ancestral metabolisms and are unlikely to gain mutations to overcome these fitness differences. In spite of these challenges, we do find that they may be more robust in the face of environmental perturbations at least in comparison with the ancestral host metabolism lineages. Our results provide a critical set of null models and expectations for understanding the forces that shape the structure of prokaryotic life.

evolutionary biology↗

bioRxiv2022

Out of the blue: the independent activity of sulfur-oxidizers and diatoms mediate the sudden color shift of a tropical river

Rio Celeste ("Sky-Blue River") is a river located in the Tenorio National Park (Costa Rica) that has become an important hotspot for eco-tourism due to its striking sky-blue color. A previous study suggested that this color is not caused by dissolved chemical species, but by precipitation of lightscattering aluminosilicate particles at the mixing point of two colorless streams, the acidic Quebrada Agria and the neutral Rio Buenavista. We now present microbiological information on Rio Celeste and its two tributaries, as well as a more detailed characterization of the particles that occur at the mixing point. Our results overturn the previous belief that the light scattering particles are formed by the aggregation of smaller particles coming from Rio Buenavista, and rather point to chemical formation of hydroxyaluminosilicate colloids with Quebrada Agria as the main contributor to the phenomenon, with Rio Buenavista acting as a secondary source of silica to the reaction. We also show how the sky-blue color of Rio Celeste arises from the tight interaction between chemical and biological processes. Sulfur-oxidizing bacteria generate an acidic environment in Quebrada Agria, which in turn cause dissolution and mobilization of aluminum and other metals, while in Rio Buenavista the growth of diatoms transforms dissolved silicon into colloidal biogenic forms. The local interaction between these two well-known biological activities gives rise to the unique Rio Celeste phenomenon, in what constitutes a textbook example of emergent behavior in environmental microbiology.

microbiology↗