Mechanisms of Evolutionary Innovation Point to Genetic Control Logic as the Key Difference Between Prokaryotes and Eukaryotes

A qualitative assessment of limits of active flight in low density atmospheres

Exoplanet atmospheres are expected to vary significantly in thickness and chemical composition, leading to a continuum of differences in surface pressure and atmospheric density. This variability is exemplified within our Solar System, where the four rocky planets exhibit surface pressures ranging from 1 nPa on Mercury to 9.2 MPa on Venus. The direct effects and potential challenges of atmospheric pressure and density on life have rarely been discussed. For instance, atmospheric density directly affects the possibility of active flight in organisms, a critical factor since without it, dispersing across extensive and inhospitable terrains becomes a major limitation for the expansion of complex life. In this paper, we propose the existence of a critical atmospheric density threshold below which active flight is unfeasible, significantly impacting biosphere development. To qualitatively assess this threshold and differentiate it from energy availability constraints, we analyze the limits of active flight on Earth, using the common fruit fly, Drosophila melanogaster, as a model organism. We subjected Drosophila melanogaster to various atmospheric density scenarios and reviewed previous data on flight limitations. Our observations show that flies in an N2-enriched environment recover active flying abilities more efficiently than those in a helium-enriched environment, highlighting behavioral differences attributable to atmospheric density vs. oxygen deprivation.

Physical constraints during Snowball Earth drive the evolution of multicellularity

Molecular and fossil evidence suggests that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe. During this period, environmental conditions-such as seawater temperature and the availability of photosynthetically active light in the oceans-likely changed dramatically. Such changes would have had significant effects on both resource availability and optimal phenotypes. Here, we construct and apply mechanistic models to explore (i) how environmental changes during Snowball Earth and biophysical constraints generated selective pressures, and (ii) how these pressures may have had differential effects on organisms with different forms of biological organization. By testing a series of alternative-and commonly debated-hypotheses, we demonstrate how multicellularity was likely acquired differently in eukaryotes and prokaryotes owing to selective differences on their size due to the biophysical and metabolic regimes they inhabit: decreasing temperatures and resource availability instigated by the onset of glaciations generated selective pressures towards smaller sizes in organisms in the diffusive regime and towards larger sizes in motile heterotrophs. These results suggest that changing environmental conditions during Snowball Earth glaciations gave multicellular eukaryotes an evolutionary advantage, paving the way for the complex multicellular lineages that followed.

A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity

"Complex multicellularity," conventionally defined as large organisms with many specialized cell types, has evolved five times independently in eukaryotes, but never within prokaryotes. A number of hypotheses have been proposed to explain this phenomenon, most of which posit that eukaryotes evolved key traits (e.g., dynamic cytoskeletons, alternative mechanisms of gene regulation, or subcellular compartments) which were a necessary prerequisite for the evolution of complex multicellularity. Here, we propose an alternative, nonadaptive hypothesis for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, the evolution of multicellularity greatly reduces the effective population size (Ne) of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, providing additional raw genetic material for subsequent multicellular innovation, while prokaryotes generally face genomic erosion. Taken together, we hypothesize that these idiosyncratic lineage-specific evolutionary dynamics play a fundamental role in the long-term divergent evolution of complex multicellularity across the tree of life.

Evolution of default genetic control mechanisms

We present a model of the evolution of control systems in a genome under environmental constraints. The model conceptually follows the Jacob and Monod model of gene control. Genes contain control elements which respond to the internal state of the cell as well as the environment to control expression of a coding region. Control and coding regions evolve to maximize a fitness function between expressed coding sequences and the environment. The model was run 118 times to an average of 1.4∙10⁶ ‘generations’ each with a range of starting parameters probed the conditions under which genomes evolved a ‘default style’ of control. Unexpectedly, the control logic that evolved was not significantly correlated to the complexity of the environment. Genetic logic was strongly correlated with genome complexity and with the fraction of genes active in the cell at any one time. More complex genomes correlated with the evolution of genetic controls in which genes were active (‘default on’), and a low fraction of genes being expressed correlated with a genetic logic in which genes were biased to being inactive unless positively activated (‘default off’ logic). We discuss how this might relate to the evolution of the complex eukaryotic genome, which operates in a ‘default off’ mode.

The Astrobiology of Alien Worlds: Known and Unknown Forms of Life

Most definitions of life assume that, at a minimum, life is a physical form of matter distinct from its environment at a lower state of entropy than its surroundings, using energy from the environment for internal maintenance and activity, and capable of autonomous reproduction. These assumptions cover all of life as we know it, though more exotic entities can be envisioned, including organic forms with novel biochemistries, dynamic inorganic matter, and self-replicating machines. The probability that any particular form of life will be found on another planetary body depends on the nature and history of that alien world. So the biospheres would likely be very different on a rocky planet with an ice-covered global ocean, a barren planet devoid of surface liquid, a frigid world with abundant liquid hydrocarbons, on a rogue planet independent of a host star, on a tidally locked planet, on super-Earths, or in long-lived clouds in dense atmospheres. While life at least in microbial form is probably pervasive if rare throughout the Universe, and technologically advanced life is likely much rarer, the chance that an alternative form of life, though not intelligent life, could exist and be detected within our Solar System is a distinct possibility.

The Power Without the Glory: Multiple Roles of Hydrogen Peroxide in Mediating the Origin of Life

The hydrogen peroxide (HP) crucible hypothesis proposed here holds that life began in a localized environment on Earth that was perfused with a flow of hydrogen peroxide from a sustained external source, which powered and mediated molecular evolution and the protocellular RNA world. In this article, we consolidate and review recent evidence, both circumstantial and tested in simulation in our work and in the laboratory in others' work, for its multiple roles in the evolution of the first living systems: (1) it provides a periodic power source as the thiosulfate-hydrogen peroxide (THP) redox oscillator, (2) it may act as an agent of molecular change and evolution and mediator of homochirality, and (3) the THP oscillator, subject to Brownian input perturbations, produces a weighted distribution of output thermal fluctuations that favor polymerization and chemical diversification over chemical degradation and simplification. The hypothesis can help to clarify the hero and villain roles of hydrogen peroxide in cell function, and on the singularity of life: of necessity, life evolved early an armory of catalases, the continuing, and all-pervasive presence of which prevents hydrogen peroxide from accumulating anywhere in sufficient quantities to host a second origin. The HP crucible hypothesis is radical, but based on well-known chemistry and physics, it is eminently testable in the laboratory, and many of our simulations provide recipes for such experiments.

The timetable of evolution

The integration of fossils, phylogeny, and geochronology has resulted in an increasingly well-resolved timetable of evolution. Life appears to have taken root before the earliest known minimally metamorphosed sedimentary rocks were deposited, but for a billion years or more, evolution played out beneath an essentially anoxic atmosphere. Oxygen concentrations in the atmosphere and surface oceans first rose in the Great Oxygenation Event (GOE) 2.4 billion years ago, and a second increase beginning in the later Neoproterozoic Era [Neoproterozoic Oxygenation Event (NOE)] established the redox profile of modern oceans. The GOE facilitated the emergence of eukaryotes, whereas the NOE is associated with large and complex multicellular organisms. Thus, the GOE and NOE are fundamental pacemakers for evolution. On the time scale of Earth's entire 4 billion-year history, the evolutionary dynamics of the planet's biosphere appears to be fast, and the pace of evolution is largely determined by physical changes of the planet. However, in Phanerozoic ecosystems, interactions between new functions enabled by the accumulation of characters in a complex regulatory environment and changing biological components of effective environments appear to have an important influence on the timing of evolutionary innovations. On the much shorter time scale of transient environmental perturbations, such as those associated with mass extinctions, rates of genetic accommodation may have been limiting for life.

The Cosmic Zoo: The (Near) Inevitability of the Evolution of Complex, Macroscopic Life

Life on Earth provides a unique biological record from single-cell microbes to technologically intelligent life forms. Our evolution is marked by several major steps or innovations along a path of increasing complexity from microbes to space-faring humans. Here we identify various major key innovations, and use an analytical toolset consisting of a set of models to analyse how likely each key innovation is to occur. Our conclusion is that once the origin of life is accomplished, most of the key innovations can occur rather readily. The conclusion for other worlds is that if the origin of life can occur rather easily, we should live in a cosmic zoo, as the innovations necessary to lead to complex life will occur with high probability given sufficient time and habitat. On the other hand, if the origin of life is rare, then we might live in a rather empty universe.