Biology subjects

Ratcliff, W.

Publications and source records attributed to Ratcliff, W..

7 recordsLinked to original sources

bioRxiv2026

41% of Gram-negative bacteria encode a Type Six Secretion System

The type six secretion system (T6SS) is a highly studied, versatile bacterial nanoweapon that is important in bacterial pathogenesis and evolution. Despite extensive study, its prevalence remains poorly quantified. Analyzing 35,467 representative genomes, we find that approximately 41% of genomes in the average well-sampled Gram-negative genus (more than 30 sampled genomes) encode a T6SS. Further, we show that the distribution of the T6SS is patchy at all taxonomic levels. The uneven distribution we found is consistent with context-dependent selection, repeated evolutionary loss, or greater evolutionary lability. Our dataset provides a foundation for studying the drivers of T6SS distribution, and our pipeline enables similar surveys of other secretion systems, gene clusters, and multi-protein complexes across bacteria.

microbiology↗

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

De-Darwinizing the proteome: the genome as the original germ line

A hallmark of evolutionary transitions in individuality is the suppression of lower-level Darwinian dynamics through germ-soma specialization. The RNA world hypothesis posits that early life arose through ribozymes, RNA molecules that functioned as both catalysts and hereditary units, housed within protocells. This dual role is the chief appeal of the RNA world framework, because it makes ribozymes capable of open-ended Darwinian evolution. It is also its chief liability. Each ribozyme is a fully Darwinian entity: it replicates, accumulates mutations via Mullers ratchet, and can be displaced by selfish variants that replicate faster but contribute less to collective function. We show that between-protocell selection, even when strong, cannot overcome this within-cell evolutionary erosion, particularly as protocells evolve increased complexity by increasing the number of ribozyme types they contain. The origin of a low-copy-number informational RNA genome, translated by an ancient ribosome into protein enzymes, resolves this conflict by producing a functional workforce that is non-heritable. Protein-based enzymes are intrinsically stripped of evolutionary agency, confining heritable variation to the genome and entrenching the protocell as the primary level of Darwinian individuality. The genome, in this view, is not merely a storage device but the original germ line, and its origin marks the point at which cellular life became capable of open-ended growth in complexity.

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↗

bioRxiv2024

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.

evolutionary biology↗

bioRxiv2023

Experimental evolution of multicellularity via cuboidal cell packing in fission yeast

The evolution of multicellularity represents a major transition in lifes history, enabling the rise of complex organisms. Multicellular groups can evolve through multiple developmental modes, but a common step is the formation of permanent cell-cell attachments after division. The characteristics of the multicellular morphology which emerges has profound consequences for the subsequent evolution of a nascent multicellular lineage, but little prior work has examined these dynamics directly. Here we examine a widespread yet understudied emergent multicellular morphology: cuboidal packing. Extinct and extant multicellular organisms across the tree of life have evolved to form groups in which spherical cells divide but remain attached, forming approximately cubic subunits. To experimentally investigate the evolution of cuboidal cell packing, we used settling selection to favor the evolution of simple multicellularity in unicellular, spherical Schizosaccharomyces pombe yeast. Multicellular clusters with cuboidal organization rapidly evolved, displacing the unicellular ancestor. These clusters displayed key hallmarks of an evolutionary transition in individuality: groups possess an emergent life cycle driven by physical fracture, group size is heritable, and they respond to group-level selection via multicellular adaptation. In 2/5 lineages, group formation was driven by mutations in the ACE2 gene, preventing daughter cell separation after division. Remarkably, ACE2 mutations also underlie the transition to multicellularity in Saccharomyces cerevisiae and C. galabrata, lineages last shared a common ancestor >300 million years ago. Our results provide insight into the evolution of cuboidal cell packing, an understudied multicellular morphology, and highlights the deeply convergent potential for a transition to multicellular individuality within fungi.

evolutionary biology↗