Mass extinction

While extinction of population, genetic lineages or entire species are a common occurrence in the history of life, mass extinctions - brief times of crisis where both the amount and diversity of life sharply drop - are few events of huge importance that shape the history of a planet.

Despite the huge capacity for adaptation displayed by life, a rapid change in environmental conditions can bring the general extinction rate far above the speciation rate. Since the vast majority of biomass and biodiversity are found in bacteria, it's likely that not even the most catastrophic event can significantly dent Earth's biosphere, but it can still have grave consequences on its most evident part, macroscopic animals and plants.

Historical mass extinctions
In the Phanerozoic Eon, distinguished by the abundant presence of large-sized animals and plants, five major mass extinctions have been identified, with different causes and severity:
 * 1) The End Ordovician extinction (450-440 Ma) involved more than a hundred families of marine invertebrates, and the total victim count is estimated about 27% of all families, 57% of all genera and 60-70% of all species. A great reduction of early reef has been observed, along with a crisis of brachiopods, bryozoans, conodonts, trilobites and graptolytes. The most likely cause is the southwards movement of Gondwana, which triggered an ice age and thus caused the sea level to fall, destroyed habitats worldwide.
 * 2) The Late Devonian extinction (375-360 Ma) destroyed 19% of families, 50% of genera and 70% of species. It saw a great reduction of trilobites, graptolytes, brachiopods, placoderms; armoured jawless fish disappeared entirely; there was, again, a crisis of reefs, composed by organisms with a calcium-rich skeleton, because of accumulation of magnesium in seawater (they'll be replaced by aragonite-rich reefs). Another global cooling episode is suspected, perhaps triggered by a meteor impact; the magnesium raise, and a strong eutrophication, could have been produced by the formation of the first forests.
 * 3) The End Permian extinction (251 Ma), the largest one, destroyed 57% of families, 83% of genera and maybe 90-96% of marine species. Trilobites and most therapsids (then the dominant vertebrates) disappeared entirely, while brachiopods, mollusks, echinoderms, corals, fish, amphibians, reptiles, insects and plants are merely heavily damaged. The formation of Pangaea (which produced desertification and ecosystem mixing) is probably responsible, along with an ice age, probably the huge lava emission from the Siberian Traps and maybe an exhalation of methane from the oceanic clathrates (see below).
 * 4) The End Triassic extinction (205 Ma) destroyed 23% of families, 48% of genera and 70-75% of species. Biodiversity had not entirely recovered from the previous mass extinction; several groups of reptiles and amphibians disappear, opening the way to dinosaurs. Its cause is still unknown: volcanic events connected to Pangaea breakup are suspected.
 * 5) The End Cretaceous extinction (65 Ma) destroyed 17% of families, 50% of genera and 75% of species. Victims include most mollusks (such as ammonites) and reptiles (plesiosaurs, mosasaurs, pterosaurs and dinosaurs, except for birds); mammals, birds, crocodiles and small-sized reptiles are not heavily damaged. This extinction has been ascribed to the Chicxulub meteor impact in Mexico, and perhaps the volcanic activity of the Deccan Traps.

Consequences of mass extinctions
After a mass extinction has taken its toll, bringing death on a great deal of species, it opens up spaces that were previously occupied and/or creates new niches that were non-existent because conditions were inhibited by previous organisms. Life then slowly but surely begins to recover, starting with pioneer organisms (fern spikes are a common marker of mass extinctions). Bouncing back, however, is difficult and it takes thousands, if not millions, of years to bring about an ecosystem of at least somewhat similar properties and liveability of its predecessor.

A biotic crisis clears the way for not only new species but also new sorts of habitats, affecting the Earth as a whole and causing the planet itself to change its variables. Climate is the most common factor altered by an extinction event, although effects on other circumstances are more unlikely but not unthinkable such as the change of the world's magnetic poles or the stimuli to a greater incidence of volcanic activity or tectonic geology.

Life usually gets the better out of a disaster, not only surviving but also innovating with the ever-increasing ingenuity, creativity and cleverness that belongs to nature, making animals and plants cross new milestones and advance in complexity, design and efficiency, toughening it even further to the next catastrophe and increasing the likeliness of withstanding another calamity, at times worse than anything that came before.

Possible causes of mass extinctions
The causes of mass extinctions can be many, and varied. The events listed below can be very common (eleven basaltic floods, twelve sea-level falls and at least one major asteroid impact have been recognised in the Phanerozoic), but usually they're not enough to induce a worldwide crisis of biodiversity; rather, these occur when several events overlap. Often, however, one of these events can trigger another, causing a catastrophic chain reaction of multiple disasters.

Biogical causes

 * Keystone species disappearance can be a cause for localized mass extinctions on a relatively small scale. Keystone species have a disproportionately large effect on their environment relatively to their biomass or productivity: for example, sea otters, that protect kelp forests by eating sea urchins; the australian plant Banksia prionotes, that for most of the year is the only food source for pollinators that, in turn, are vital for other plants; prairie dogs' tunnels aerate the ground and store rain water. The extinction of one of this species due to some small event (say, an aggressive parasite) can cause the collapse of an entire ecosystem.
 * Hydrogen sulphide eruptions can be produced by sulfate-reducing bacteria, whose metabolism, promoted by warm conditions and lack of oxygen, releases large amounts of hydrogen sulfide. This gas is extremely toxic for most oxygen-breathing organisms and weakens the ozone layer. The End Permian extinction probably saw this happening because of the strong anoxia.
 * Methane production can occur by metabolic processes such as the hydrogenation of carbon dioxide or from the fermentation of plant matter; vast populations of large-sized herbivores can release huge amounts of methane in the atmosphere. Methane is an extremely strong greenhouse gas, and can induce global warming. It's now thought that methane production from herbivore sauropods had a significant role in the Mesozoic warming of Earth.
 * Eutrophication is the effect of a large amount of nutrients, such as nitrates and phosphates, released in an environment, especially aquatic. Estuaries are by nature eutrophic, as they receive nutrients from rivers. The greater biomass can consume oxygen causing anoxia and death for oxygen-breathing organisms, which are replaced by algae and bacterial masses. It's usually a local event, but the formation of the first forests (and thus disgregation of the soil, and percolation of more nutrients in rivers) is suspected to have contributed to the Late Devonian extinction.

Climatological causes

 * A sea-level fall can be caused by the production of new crust when a supercontinent is present, or when large ice caps remove liquid water from the oceans; it can leave uncovered several continental shelves, the most productive part of oceanic ecosystems, and block sea currents, causing a greater temperature difference between latitudes. The extension of continents inreases the internal area more than the coastline length, blocking both inland rainfall and the flow of nutrients seawards. It's associated with all the five great extinctions. Sea level rising, conversely, can be destructive to coastal environments and in other local cases, but it has ultimately a positive effect on global biodiversity.
 * A strong global cooling can force latitude zones towards the Equator, increasing competition, and promotes cold biomes with lesser biodiversity and productivity. Glaciation cycles have a lower impact, but they can periodically lower the sea level of several tens of metres; besides, a colder climates supports larger organisms and thus smaller, less varied populations. It can be caused by the astronomical Milankovitch cycles or by the collocation of a continent at a pole, which allows the glaciers to grow more. A global cooling occurred in Ordovician, Devonian and Early Permian.
 * Global warming has, of course, the opposite effect: it can extend tropical biomes (promoting biodiversity and productivity) and raising sea levels worldwide (which is only destructive locally and in the short term), but also contribute to ocean anoxia. It can be caused by equatorial sea currents and by greenhouse effect, where gases such as water vapour, carbon dioxide, methane, nitrous oxide (N2O) and ozone trap heat in the atmosphere. The Late Permian and Triassic saw a strong global warming.
 * Runaway greenhouse effect is an extreme consequence of self-feeding global warming: rising temperatures increase water evaporation, liberation of methane from clathrates and the turning of light-reflecting ice into light-absorbing water or vegetation. It can lead to the complete evaporation of ocean and a temperature raise of hundreds of degrees, which would effectively sterilize a planet. This is what happened to Venus, which for this reason is hotter than Mercury despite being farther from the Sun.
 * Anoxia is the scarcity or absence of free, breathable oxygen in seawater. It can be caused by strong global warming (becoming global if the worldwide average temperature rises above 25°C) and by high concentrations of carbon dioxide, as it happened at the end of the Permian. The lack of oxygen, starting from deep sea and moving upwards, is catastrophic for marine communities, including bacteria, and it can block the accumulation of calcium carbonate necessary for shells and carapaces. Usually, anoxic events last less than a million years; they've probably occurred in Ordovician, Permian and Triassic.
 * An oceanic overturn is the interruption of the circulation that makes surface seawater (richer in salt and thus denser) to sink, and the deep, anoxic water to rise, bringing oxygen in the deep sea; when this happens, oceans stratify and anoxia can extend to the surface. It can occur at the end of a glaciation, where ice melting creates large masses of oxgen-poor fresh water. It could have played a role in the Devonian and Permian.

Geological causes

 * A basaltic flood can originate from the emission, over thousands of years, of a huge amount of basaltic lava with low viscosity, usually from the fissures between tectonic plates. The lava can cover hundreds of thousands of square kilometres; besides the direct destruction of the flooded area, it's accompanied by particulate (which can block solar light, inhibiting photosynthesis), sulfur oxides (that cause extensive acid rains) and carbon dioxide (that can cause global warming once the particulate has disappeared). Two basaltic plateaux (the Deccan Traps in India, 500 000 km2, and the Siberian Traps in Russia, 1.5 million km2) are directly connected to the End Cretaceous and End Permian extinctions.
 * Clathrate hydrates are minerals where a lattice of porous ice traps pockets of gas: clathrates containing methane are found in permafrost. Methane clathrates, melting in response to warming conditions, can release billions of tons of methane, increasing the greenhouse effect. It probably happened during the Permian extinction, and it might happen again in the close future.
 * Plate tectonics can damage biodiversity by bringing together continental masses, through different mechanisms: the larger area causes desertification on the inside and less nutrients on the coastline; it increases competition and amalgamations (as it occurred when the Americas linked, causing the collapse of the South American fauna); it lets oceanic crust grow old and sink, lowering the sea level. This all happened with Pangaea in the Permian and Triassic.
 * A geomagnetic reversal is an inversion, for reasons unknown, of Earth's magnetic field: more specifically, it inverts the position of the magnetic north and south pole. Each reversal is unpredictable (the last ones occurred 780 000 years ago and 2 million years before, but in the Cretaceous none happened for tens of millions of years), and there is a transition phase lasting 1000-10 000 years, in which the magnetic field is very weak, leaving the surface more exposed to cosmic radiations. An increase of the global volcanic activity is also suspected.

Astronomical causes

 * A sufficiently large asteroid or comet impact (at least a few km of diameter) can have immediate traumatic effects (seismic shock, tidal waves, wildfires, debris fall) and release a combination of particulate, carbon dioxide and sulfur oxides similar to that produced by basaltic floods, with similar effects. The impact of an asteroid in the Gulf of Mexico is believed to be the main cause (though probably not the only one) of the End Cretaceous extinction.
 * A wearing of the ozone layer can be caused by a high atmospheric concentration of halogens (fluorine, chlorine, bromine, almost all of them produced by human activity); hydrogen sulfide eruptions have the same effect. It allows UV light and cosmic radiations to reach the surface, with direct and adverse biological effects (e.g. skin and eye cancer) and can promote the formation of new ozone on the surface, where it's highly toxic.
 * A gamma-ray burst is a rare and extremely violent emission of gamma rays and other radiations, usually lasting a few seconds, produced by the collapse of a massive black hole or neutron star; they're estimated to occur every few million years per galaxy. A gamma-ray burst closer than 6000 light-years can destroy the ozone layer partially or entirely and heavily irradiate the surface of a planet, effectively killing most organisms that are not underground or underwater. It's speculated to have happened in the Ordovician.

Examples in speculative biology

 * The third part of TFIW takes part long after a large mass extinction, 200 million years in the future.
 * At least two major mass extinctions are provoked by human activity in Man After Man - one in the immediate future and one after the return on Earth of space-travelling humans, 5 million years after.
 * Most alternate evolution projects have a mass extinction or lack of one as point of divergence. The most popular, found in The New Dinosaurs and Spec, is the lack of the KT extinction.