Before the Phanerozoic

In the beginning, space was expanding and doing so incredibly fast. It was cosmic inflation, a process in which the fabric of space itself enlarged exponentially. When it stopped, all the energy fueling it promoted excitations of various quantum fields, creating particles and antiparticles. A hot, dense, but still expanding Universe emerged: the Big Bang happened. After this grand event, some 13.8 billion years ago, matter (which prevailed over antimatter for not completely understood reasons) started to coalesce into stable atoms and then molecules. Natural density variations, products of quantum fluctuations stretched during the period of inflation, gave rise to aggregation points that eventually formed stars and galaxies. One of these galaxies was the Milky Way, where, in one of its spiral arms, a planetary system was starting to take shape approximately 4.5 billion years ago, a result of a disturbance in a cloud of cosmic dust and gas.

Most of the mass was concentrated into one body, which started collapsing onto itself due to its own gravity and, under amazing pressures, began nuclear fusion, transforming hydrogen into helium, releasing tremendous amounts of radiation: the Sun was born. The disk of remnant material around the young star formed clumps some of which would become the eight known planets of today, with one of these being a rocky world known as Earth. Not long after its appearance, a protoplanet called Theia hit Earth, prompting the formation of the Moon, a result of the ejected debris from the violent impact. Soon after this event, the Earthly environment started to change drastically.

As our planet cooled and its crust solidified, great quantities of greenhouse gases, such as carbon dioxide, were released into the atmosphere, which kept temperatures high. At the same time, however, it is possible very magnesium-rich rocks, apt for sequestering the aforementioned gases, were brought to the surface by a rapidly recycling chemically heterogeneous mantle (with a high proportion of water) that promoted quick movement of tectonic plates (note these plate tectonics probably functioned a bit differently compared to modern ones and when exactly this geological feature developed is a topic of contention), which play important roles in the carbon cycle still today. This movement, generating the absorption of the greenhouse gases, allowed the decrease of temperatures and the development of conditions more like the ones of the present. Oceans, though, had already emerged even before the depletion of the greenhouse atmosphere, since volatiles, like water and several gases, were pumped into the atmosphere by the mantle, and the high air pressure allowed water to stay in the liquid phase. 

To fathom the importance of these geological motions, one can look to Venus. Due to its closer proximity to the Sun, it is believed that the planet's warmer surface hindered continued cycles of crust damage, which eventually helped lead to the spread of the plate tectonics found on Earth and exclusively on it, nowhere else in the Solar System (at least in the present). This lack of plates may have proved catastrophic, for the great amounts of carbon dioxide and other gases released in the atmosphere by extensive volcanism (similar to massive volcanic events of our own planet, such as the ones participating in extinctions in the Devonian, the Permian, and the Triassic) were not sufficiently absorbed and accumulated. It has also been appointed that powerful impacts during the planet's formation could have superheated its core, fueling its aforementioned volcanism that remains to the present day.

The rises in temperatures originating from the emitted greenhouse gases promoted the evaporation of the oceans that possibly bathed the land of the, until then, perhaps temperate and potentially even habitable celestial body, which would have been achievable due to a dimmer early Sun, an initially way thinner atmosphere and a hypothetical magnetic field (associated with the effects, on the core, of the previously cited energetic collisions), not as long-lasting as Earth's (mentioned in more detail in this chapter). The water vapor arising from the theorized water bodies maybe contributed even more to what had become a particularly intense runaway greenhouse effect, one which would culminate in the hellish planet of today, bearer of an atmosphere so thick little sunlight gets to the ground. 

And it is this substantial envelope of gas the reason the planet managed to escape tidal locking (it is, therefore, the cause for the Venusian rotation being so slow and feasibly the cause for it being from east to west, instead of west to east like observed in most other planets of our system), a phenomenon which can result, over millions of years, in an object having its rotational and orbital periods synchronized due to strong gravitational interactions, leaving it permanently facing the other object it orbits with only one side and viable in Venus' cases due to its distance to the Sun (the Moon, for example, is tidally locked to Earth and Mercury, while not tidally locked in the strict sense, is subject to a different type of locking in which it completes three rotations every two revolutions, an arrangement stabilized by its orbit's high eccentricity).

The primordial Venus being subject to a tidal locking process (which would have progressively slowed its rotation) due to lacking its modern, thickened atmosphere makes it cogitable it was never "life-friendly" in the first place as well, an idea growing ever more accepted: cloud distributions between the day and night sides may have created a greenhouse effect that never allowed enough temperature decrease for the formation of the aforementioned oceans. The fast rotation of Earth, on the contrary, would have stabilized oceans by allowing them to cool effectively. Not only that, but the faint young Sun, previously alluded to as one of the factors that could have theoretically permitted Earth's sister world to be habitable, probably also allowed for these oceans to condense from the water vapor in the first place, a process described at the beginning of this entry and which maybe could have not been possible if the star was as luminous as it is today. As such, if any life developed during Venus' conceivable, but probably never-existent Eden remains a mystery and so does if any, if even managing to come to be in the first place, survived the volcanic cataclysm described.

Returning to our planet, the magnesium-rich rocks would also play another important role by favoring the production of deep-sea hydrothermal vents of the cooler type, which might have served as the origin point for early, primitive life, which could have emerged as early as around 4.3 billion years ago. These vents, while providing a potential energy source via their efflux of hydrogen coupled to redox reactions, may not only have served as concentration points for several organic compounds (like nucleotides and fatty acids) but may have also contributed to the formation of RNA molecules, which could, acting in conjunction with amino acids (building blocks of proteins), have been the foundation of initial lifeforms, although these were maybe based on other components. This association between RNA and amino acids may have kickstarted the origin of the present genetic code (which is not completely universal, meaning the amino acids correspondent to certain sets of nucleotides vary between certain organisms) and of RNA translation, both of which are crucial for life due to coordinating protein synthesis. 

These initial amino acid-RNA complexes could have worked in a loop-like manner: specific enzymes, themselves made up of amino acids, would interact with the nucleotides in RNA and allow them to bond with other amino acids to create more amino acid chains, which, for their part, would develop once again into those specific enzymes, completing the cycle. This primordial process akin to modern RNA translation would have been gradually refined, more precisely distinguishing amino acids and sequences of nucleotides, eventually arriving at the present genetic code of 20 amino acids. Besides, it has been suggested that modified nucleotides (still found in RNA and DNA, with a wild range of functions) enabled the emergence of chimeric structures made out from the "fusion" of RNA and amino acids, explaining how these associations came to be in the first place, associations which could have eventually transformed into the familiar ribosomal protein synthesis of today. 

Curiously, amino acids and nitrogenous bases (components of nucleotides) forming hybrid structures might have, moreover, laid the foundation for the replication of genetic material seen in all life (based on base pairing and nucleotide polymers, like RNA and DNA) when acting as primordial, self-replicators functioning independently of the just cited base-pairing. It has also been experimentally shown that RNA replicators could have readily diversified into distinct lineages, some turning parasitic by losing the "instructions" for the production of replication machinery, some reproducing faster than others, some even cooperating, but all interacting, albeit indirectly, among themselves in a way that equilibrium was reached and to the point that the extinction of one RNA replicator meant the extinction of several others.

It is important to mention that nucleotides, required to assemble both RNA and DNA, their amino acids companions, and even sugars were possibly extraterrestrial in origin, being predicted to be capable of forming in cosmic dust and then carried over by meteorites, despite the fact that an Earthly origin might have also occurred concomitantly. These complexes of RNA and peptides (aggregations of amino acids) would have been encapsulated by self-assembling vesicles of fatty acids, which were also promoted by the characteristic environment of the hydrothermal vents and apparently were stabilized by interacting with both the RNA and the amino acids. And with that, the first protocells came into existence, with the fatty acids gradually replaced by phospholipids posteriorly, with intermediate, blended membranes that could have favored protocellular processes (by being permeable to compounds modern cell membranes are not for instance). 

It is even possible that this replacement by phospholipids occurred as an early product of natural selection, as protocells capable of synthesizing these lipids would have grown at the expense of neighboring vesicles lacking or having less amounts of them, apart from becoming capable of colonizing new environments. Interestingly, it is thought this synthesis of membrane components was one of the main factors behind protocell division, since the increased temperature inside the protocell as a result of its metabolism stimulated the transfer of these components to the membrane itself, promoting its growth and, in due course, its fission, generating one more protocell (this can still be somewhat observed, although there are many and significant differences, in eukaryotic cells, in which temperature variations are correlated with mitosis and mitochondrial activity, a source of heat).

During these initial moments, a set of specific proteins known as prions and prion-like forms, originating naturally from the amino acids present in the habitat, may have aided the formation of the first lifeforms, due to their abilities to protect RNA, carry information, withstand harsh conditions, sequester nucleotides to facilitate the polymerization of the cited RNA, among other capabilities, invoking once again the intense relationship between amino acids and nucleotides that may have kickstarted living things. In the modern world, prions are found in bacteria, in various eukaryotes, in other archaea, and even in viruses (a reality that can be explained by their potential importance in life's beginning, their presence in these various organisms being a relic of the past), and their misfolded versions, capable of transforming normal forms into misfolded versions as well, are responsible for severe, lethal diseases in some mammals, including humans.

Even today, hydrothermal vents serve as literal hotspots for life, providing essential energy in abyssal environments far removed from the Sun's influence. And the life they harbor is by no means only unicellular, as many animals call them home, amazing examples of complex life returning to their humble possible origin much later. A few of such animals are polychaete worms (aquatic annelids more mentioned here) of the family Siboglinidae (possibly originating reasonably early in the Paleozoic), which includes the giant tubeworm (Riftia pachyptila), an animal that lives inside an up to 2-meter-long tube composed of chitin (a structural carbohydrate mentioned once again in the next entry) and that completely lacks a digestive system. Instead, it counts with a specialized organ housing intracellular bacteria of the class Gammaproteobacteria (phylum Proteobacteria) that metabolize the hydrogen sulfide pumped out by the vents, producing crystallized sulfur and carbon-based compounds that can be utilized by the worm itself. In order to constantly deliver the hydrogen sulfide and also oxygen to the bacteria, it has a bright-red, bushy plume that usually sticks out from the tube, in stark contrast to its otherwise pale body. It displays such a crimson complexion because it is full of extracellular hemoglobin (also utilized by other annelids, such as earthworms), which binds the two molecules and transports them to prokaryotes living in its interior, a mutually beneficial arrangement in which the bacteria dwell in a protected habitat and the invertebrate gets nourishment. Since vents are, despite all of their importance, quite unstable, not lasting for many years, the giant tubeworm grows fast, starting life as a mobile larva that eventually settles and starts constructing its tubular home, but capable of dispersing far before doing so, essential for seeking out new possible habitats for when the one it came from inevitably ends.

Close to 4 billion years ago, probably lived the Last Universal Common Ancestor (LUCA), from which sprouted the two domains of cellular life already briefly mentioned: Bacteria and Archaea. LUCA, probably quite similar to bacteria and many archaea, may have lived close to hydrothermal vents as well, being a potentially autotrophic anaerobe (living from the gases carbon dioxide, hydrogen, and perhaps nitrogen, with its metabolites helping fuel other neighboring organisms, which left no living descendants) that possibly already employed DNA, more advantageous than RNA for storing genetic information due to, among other factors, its increased stability, even though RNA still plays paramount roles in the functioning of organisms that utilize DNA, so much so that it is possible to consider the RNA world still a reality. How the transition from RNA to DNA took place remains mysterious, as with many, if not most topics within this subject. With that being said, it has been shown that ribozymes (RNAs with enzymatic activity) can, alone, replicate themselves, not requiring associations with amino acids as previously brought up, but, additionally, they can also function as reverse transcriptases (enzymes that transform RNA into DNA), being capable of incorporating DNA nucleotides from the environment and forming DNA strands complementary to RNA strands, maybe serving, consequently, as one of the means by which this change took place.

Speaking about viruses in more detail, a recent idea, denominated the “chimeric-origins hypothesis” suggests that these acellular organisms, the most abundant beings on the planet, originated from primordial, parasitic RNA and DNA replicators (the former having already been mentioned). After acquiring structural protein genes from cellular beings, viral particles would have been formed: the proteic coats offering not only protection but, eventually, a pathway for entering their hosts. These parasites would then continue to exchange genetic material with cells and new forms would continue to emerge way after this initial stage, contributing to the diversity of the virosphere, which likely is polyphyletic in origin, meaning there was not a single common ancestor to all viruses, but several. Even LUCA itself likely had to contend with viruses, already exhibiting enzymes useful for degrading foreign RNA, inhibiting viral protein synthesis and, consequently, replication. 

Most commonly found in prokaryotes, plasmids, pieces of genetic material that are normally extra-chromosomal (meaning they are not part of the cell's main genome) are also potential relics of these primordial replicators. Though similar to viruses in necessitating a host cell, plasmids became more intimately intertwined with theirs, undergoing a sort of "domestication" and sequestering additional genetic material, changing and diversifying as time went by. Some of the sequestered genes confer great advantages to their hosts, guaranteeing the survival and proliferation of both. Other plasmids, however, are not so useful, constituting a burden and qualifying as parasitic. Also like viruses, plasmids too can disseminate and they can do so in various ways: they can be transmitted from mother to daughter cell during division, they can be transferred between different mature cells when these enter in contact, they can end up in the environment and be absorbed by a nearby cell, and, finally, they can even be transported by viruses between cells! These last three ways, constituting forms of horizontal gene transfer, are especially important for prokaryotic organisms for granting them genetic variability, since they are unable to reproduce through sexual means (sexual reproduction will be further explored in this entry, as well as specific means of archaeal horizontal gene transfer). Apart from these two, viroids, infective organisms consisting only of circular pieces of RNA (with such pieces coming in different shapes, being straight or branched for instance), are more remnants of these primitive habitats still in the modern day, constituting important plant pathogens (they affect plants by producing other RNAs, which interfere with normal plant metabolism: the many influences of RNA in cell functioning are also mentioned here) and many are ribozymes, thus with enzymatic activity of their own.

More or less 3.5 billion years ago, a unique group of bacteria, cyanobacteria, developed, with the most basal extant lineages appearing around 2.7 billion years ago. These lifeforms made use of oxygenic photosynthesis, using sunlight to fix carbon and releasing oxygen in the process. Other organisms had already been utilizing photosynthesis but of the anoxygenic variety, way more widespread (encompassing several phyla within Bacteria) and which exploits a myriad of compounds as electron donors, ranging from sulfide to hydrogen, to other substrates, while all oxygenic photosynthesizers employ water (this may change as a product of environmental aspects). Besides this, anoxygenic photosynthetic bacteria are also diverse in the wavelengths of light they absorb, enabling them to niche partition, occupying the same space but not necessarily competing for the same resources (electromagnetic waves in this case). The oxygenic photosynthesizers probably only lived in freshwater at first, where there was a lack of electron donors other than water itself, while the anoxygenic ones likely monopolized marine environments.

At around 3 billion years ago, Earth suffered a tremendous impact as an asteroid many times larger than the main one responsible for the fifth mass extinction of the Phanerozoic (explained here) hit the planet. These collisions at this time, however, were not rare and occurred every few millions of years. Due to this event in particular, oceans were partially evaporated and the globe was immersed in a period of darkness that proved catastrophic to surface photosynthesizers. Long term however, the catastrophe actually proved beneficial to most lifeforms, as the generated tsunamis mixed iron-rich deep waters with iron-poor superficial ones, boosting anoxygenic photosynthesizers (an association which will soon be cited again) and various archaea. Besides, the vaporization of both the asteroid and the crust it collided with injected nutrients like phosphorus and sulfur into the biosphere, fueling even more the growth of the microorganisms. Consequently, such impacts were beneficial to early Earthly life, generating blooms as previously nutrient-deficient conditions were suddenly reversed. It perhaps was a little later, some 2.5 billion years ago, when the first continents emerged due to Earth's cooling interior, even though islands originating from magma hotspots (nowadays, examples of such islands are Hawaii and Iceland) probably dotted the planet's surface since the initial condensation of its oceans.

Though initially making no significant impact in the atmosphere, things would change as cyanobacteria underwent a burst of diversification (with the advent of multicellular forms as well) some 2.4 billion years ago (give or take a few hundred million years): the Great Oxidation Event (GOE) started, which lasted until circa 2 billion years ago. The previously dominating anoxygenic photosynthetic bacteria, after depleting many of their electron donors, like ferrous iron (with its levels already getting lower due to a possible decrease in hydrothermal iron fluxes), would have created an environment conducive to cyanobacterial growth, which also would have been stimulated due to a flux of phosphorus into the bodies of water (this likely was an indirect result of volcanic activity as will soon be brought up). Methanogens, methane-producing Archaea, were also already playing a part in the oxidation of the atmosphere another way: during times of plenty, the methane they synthesized escaped to the air in great fluxes (making Earth undergo organic haze episodes that could resemble the also hydrocarbon-composed haze observed in Saturn's moon Titan). Incident UV radiation promoted the photolysis of this methane and the loss of considerable amounts of hydrogen to space, facilitating the eventual oxidation of the gassy layer surrounding our planet by the removal of reducing components. 

With that preceding situation, oxygen was now being formed abundantly and, as it got carried on by the waters, several anaerobic organisms were likely decimated en masse by the reactive substance, quite toxic to them, but the atmosphere continued with its composition of nitrogen (actually, nitrogen may have had a partial pressure higher than the one it has in the modern atmosphere), carbon dioxide, methane, and other gases. However, as oxygen reacted with various minerals, along with most of the remnant iron in the bodies of water (this prompted the precipitation of the iron formerly dissolved in water in the form of rust, but substantial amounts of iron had probably already precipitated in anoxic conditions in the form of green rust, with these two types of precipitation being the origin behind much of current iron ore deposits), which constituted sinks for the gas, it began to affect the air more expressively. Reacting with methane, it generated water and carbon dioxide, which was absorbed by the photosynthesizers and, gradually, the remnant greenhouse gases were sucked up. 

Consequently, several glacial pulses, during which Earth may have truly been completely covered in ice, succeeded (alternating cycles of methane increase and decrease may have contributed to corresponding periods of thawing and freezing), adding another deadly element to the massive extinction that had been kickstarted by the cyanobacteria’s waste products. It is also worth mentioning that reactions involving oxygen and UV radiation additionally led to the creation of the ozone layer, which, acting as a shield against certain wavelengths of solar radiation, protected oxygen itself from being degraded via reactions with light, allowing more methane to be oxidated and worsening the climate change that led to the glaciation episodes in the first place.

Volcanism probably also acted upon this scenario in two opposing ways. First, the lava emanating from the volcanoes, once cooled, would have been weathered, with carbon dioxide getting absorbed (decreasing the greenhouse effect) and with many nutrients (like phosphorus) transported into the sea, where they would have fueled the growth of cyanobacteria, contributing, thus, to increased rates of photosynthesis and, by consequence, cooling. Second, erupting volcanoes would have replenished the levels of carbon dioxide in the atmosphere and, as such, contributed to the end of the glaciation. In the same way a great influx of nutrients may have been one of the starting factors for the GOE, it appears the lack of nutrients could be one of the reasons it ended, bringing about a drastic reduction in the biosphere's overall size, ending the episode with another extinction, perhaps explaining the low oxygen levels that characterized the following 1 billion years due to a decrease in oxygenic photosynthesis.

Despite the catastrophe, the surviving life was now able to utilize oxygen in their metabolisms, which allowed for much more efficient energy production (oxygen is a great electron acceptor) and a large number of other applications. Even before the global spike in oxygen, some microorganisms had already been adapting, in more local settings, to the gas, originating both from the cyanobacteria from before the event and from abiotic processes. Due to this, many evolved antioxidant enzymes capable of dealing with the molecule and some of its byproducts: reactive oxygen species (ROS), which posed an even larger threat because of their tendency, as the name already leaves explicit, to easily react with various substances and damage cellular components. Amazingly, life did not restrict itself to eliminating ROS. Instead, it also began to take advantage of them, to the point that, today, ROS are purposely produced by many cells for use in various activities, like communication.

Like Earth, Mars also underwent an oxidation event of its own, though very distinct in cause, not arising from biotic factors. Also like our planet, Mars initially possessed a reducing atmosphere, one which allowed it, despite its bigger distance from the Sun when compared to Earth and the star's decreased brightness at the time, to spouse temperatures adequate for the existence of liquid water. Consequently, it was far from the cold and dry world it is today, being much warmer and wetter, with various active volcanoes and even hydrothermal vents. Seeing as how fast life potentially arose on our own celestial body, it is by no means far-fetched to believe Martian lifeforms thus originated during this habitable phase, a habitable phase, which, nonetheless, did not last for very long, probably ending around 3.5 billions of years ago. The oxidation event was a possible cause for this transition: the Martian surface was the first to be oxidized by a variety of means, including by ultraviolet radiation and dust storms, incremented by the planet's lower gravity. As the rocks were oxidized, giving rise to the rust seen in modern Mars, more reducing gases were released into the atmosphere, actually incrementing the greenhouse effect and leading to the evaporation of water, resulting in desertification. However, the smaller world would be unable to hold on to its atmosphere (it is still being lost to this day), thanks to its lack of a strong magnetic field (the composition of Mars' core led to the shutdown of its field hundreds of millions of years before the oxidation event, which actually increased surface oxidation in the first place by allowing the passage of more radiation due to the atmosphere stripping: more is said about the remnants of Mars' magnetosphere here), ultimately culminating in its dry and frozen fate.

Be that as it may, the poor nutrient conditions correlated with the end of the GOE likely exposed the enduring organisms to new challenges that ultimately favored the development of new traits and survival techniques. It is in such context that, about 2 billion years ago, some anaerobic archaea could have associated with aerobic bacteria (the future mitochondria) to form a relationship that benefited both, one in which the bacteria would reside inside the archaea (endosymbiosis) in a way that both could live more effectively in a habitat with limited nutritional opportunities (how exactly this endosymbiosis took place is disputed, with it being conceivable it occurred via a gradual process of interaction between the two microbes, with the archaea engulfing the bacteria by the manner of long and branching projections, as seen in modern, related archaea). These organisms would together constitute a new group: Eukarya. 

Despite this, it is important to note that the proto-eukaryotic archaea, like other members of their group (the Asgard archaea, which still count with extant representatives apart from the eukaryotes themselves), probably already counted with precursors to more complex components found in eukaryotes in the form of quite more primitive cytoskeleton and intracellular membrane systems (note that internal membranes are not at all an exclusivity of Asgard archaea, being present in other archaea and in several bacteria, with one example being the thylakoids of chloroplasts). However, it apparently was the symbiosis itself the main driver for the further sophistication of these traits (the endoplasmatic reticulum, a characteristic eukaryotic organelle, is an example of such "sophistication'', with many precursor components present in other archaea), culminating in the modern eukaryotic cells. 

Many more events of endosymbiosis, though, would also independently occur. Some eukaryotes, for instance, turned photosynthetic by acquiring cyanobacterial hosts (the future plastids, of which chloroplasts are one example). Even more amazingly, endosymbiotic processes have even involved eukaryotes consuming other eukaryotes. Some euglenids, single-celled and flagellated eukaryotic cells, for example, acquired photosynthetic activity not by associating with cyanobacteria directly, but by consuming green algae, fellow eukaryotes, an event called secondary endosymbiosis. The common ancestor of dinoflagellate algae (which can associate symbiotically with invertebrates, such as corals, as cited here and here) and apicomplexans (a phylum including protozoans that parasitize humans like Plasmodium and Toxoplasma) also participated in an event of secondary endosymbiosis, consuming red algae. In the case of the apicomplexans, the photosynthetic function of the internalized host was eventually lost. There are even instances of tertiary endosymbiosis. Additionally, endosymbiosis also happens inside multicellular organisms: most insects count with endosymbiotic bacteria, many of which live in specialized cells, called bacteriocytes, that contain and nurture them.

Just like during initial oxygen production, eukaryotes once again faced the dangers of oxygen and ROS due to an increased aerobic metabolism not only accompanying but allowing their increasing complexity (even endosymbiotic cyanobacteria present in phototrophic eukaryotes likely contributed to this "challenge", since photosynthesis also produces ROS). This possibly resulted in the evolution of the peroxisomes (organelles that started partaking in some of the aerobic metabolism of the bacterial symbiont in order to reduce ROS formation) and in meiotic sex being an ancestral eukaryotic trait (even though some members of Eukarya became asexual later), maybe deriving from strategies that had already been adopted by other archaea, which, when faced with DNA damage, congregated and transferred fragments of genetic material between themselves, a process based on recombination of homologous DNA segments that repaired the damaged material (this phenomenon is still practiced by archaeal cells today and varies between different species, with some even fusing and then dividing). 

Even in the modern world, various eukaryotic organisms, some of which usually restrict themselves to asexual reproduction in more optimal circumstances, undergo meiosis and engage in sexual reproduction when subject to stressful conditions capable of injuring DNA. Additionally, it is also possible that the nuclear membrane characteristic of eukaryotes also evolved as a protection mechanism against the increased levels of ROS (perhaps it actually originated from the original engulfing process as described earlier, but the protective function would still exist, maybe explaining the permanence of such a feature), helping protect the main genome from the products arising from the aerobic metabolism of the symbiotic bacteria and plausibly clarifying why a large number of genes from such bacteria relocated to the nucleus: simply because there they were also more protected from mutations. 

This gene migration also probably involved what can be described as an invasion of the archaeal nuclear genome by rapidly proliferating DNA segments (group II introns) that inserted themselves in the middle of protein-coding portions of the genetic material: this likely was the origin of eukaryotic, spliceosomal introns, fragments that get spliced out of the RNA when it is transcribed, while exons are fragments that remain in the transcribed RNA. It is possible that this event promoted significant instability in the host's genome, perhaps culminating in many eukaryote traits, originally developed as defense mechanisms against these mobile and multiplying invaders. Some of the traits could have been the linearization of chromosomes, the spliceosome (an RNA splicing complex that later conferred eukaryotes the capability of having multiple proteins encoded by only one gene through alternative splicing), and even another selective pressure in favor of the nucleus. Many members of Eukarya gradually lost these introns (though others gained more introns) and, in some, the spliceosome has also seen reduction, with animals and plants usually having the most and longest introns. 

A return to more nutrient-rich conditions from around 1.4 billion years ago to 800 million years ago fueled an unprecedented diversification of Eukarya, with multicellular eukaryotic organisms being part of this intense radiation of forms. Although prokaryotes (bacteria and non-eukaryotic archaea) do display multicellularity (with myxobacteria, mostly soil bacteria that come together to prey on other bacteria and fungi by secreting various harmful compounds, while also forming sometimes colorful, macroscopic fruiting bodies for dispersal when there is a lack of nutrients, being another example besides cyanobacteria), more substantially complex forms of multicellular life are an exclusivity of the eukaryotes (even though there are various instances of eukaryotic development of more simple multicellularity, occurring as early as about 1.6 billion years ago), in which several lineages became multicellular independently, like certain algae, plants, various fungi, animals, and others. Preceding eukaryotic traits may have facilitated these transitions: the nucleus, for example, allows a higher degree of gene expression regulation (more regulatory mechanisms will be explored during our stop in the Devonian), which is essential for cell differentiation and specialization and, therefore, for the rise of multicellularity. 

In multicellular eukaryotes, meiotic sex became restricted to germline cells, with somatic cells not undergoing the meiotic repair process due to it affecting gene regulation and they already being differentiated. Additionally, in these multi-celled lifeforms, meiosis would potentially aid in the "purging" of deleterious genes and mutations when gametes (usually containing half of the genetic material of somatic cells) were formed, since recessive genes, for instance, could be "unmasked" and expressed phenotypically in these reproductive cells, this being another conceivable reason meiotic sex persisted in the long path of eukaryotic evolution. 

As for our group, Animalia, it is thought that its first representatives, probably early sponges (Porifera thus likely constitutes a sister group to all other animals), originated during the Tonian or Cryogenian Periods, both of which, together, spanned from 1 billion years ago to roughly 635 million years ago. During the latter, our planet was subject once again to ice ages, with there being two moments when it was significantly colder, possibly in a state known as “Slushball Earth”, contrasting with the conceivable "Snowball Earth" of the GOE by having more significant remnants of liquid water, which provided important refugia for life. The causes for these periods of bitter coldness were likely multifactorial, like most if not all things. Increase in day length due to interactions between our planet and its moon may have promoted more photosynthetic activity, helping explain the higher levels of oxygen and the cooling not only during this period but maybe during the GOE as well. 

Additionally, the weathering of rocks resulting from volcanic activity likely helped the absorption of carbon dioxide, reducing the greenhouse effect, with this weathering also leading to a higher nutrient flux into the bodies of water, similar to what also happened during the GOE. It is even possible that a more substantial availability of specific elements during the Cryogenian triggered the diversification of both nitrogen-fixing cyanobacteria and picocyanobacteria, very diminutive cyanobacteria that do not engage in nitrogen fixation and are found throughout present aquatic ecosystems, capable of occupying spaces of quite contrasting conditions. Such diversifying microbes could have also played a part in both the processes of oxygenation and glaciation. Erupting volcanoes were, once more, presumably one of the factors behind the thaw which ended these glaciations. 

The following period, the Ediacaran, would witness the appearance of many peculiar, multicellular organisms of uncertain affinities. It is possible their appearance was correlated to a more significant spread of animals and fellow eukaryotes. Sponges, for instance, may have promoted ventilation of coastal waters, consuming high numbers of the aforementioned picocyanobacteria and, in the process, facilitating the growth of much larger eukaryotic phytoplankton, while increasing the amount of light reaching algae lower in the water column, allowing for the oxygenation of deeper areas. Besides, the bigger phytoplankton sank faster when dead, and so, aerobic decomposers, formerly consuming oxygen closer to the surface, now consumed the gas in the substrate, this possibly being another mechanism behind the greater oxygenation of the water column as a whole and one which intensified itself due to the emergence of zooplankton, such as ctenophores and cnidarians. Either way, the strange lifeforms of the Ediacaran would largely disappear and much more familiar forms would take their place with the advent of the Phanerozoic. 

Furthermore, check the sources for this entry here.

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