User:Philcha/Sandbox/Evol Host of Life (old stuff)

Removed old stuff from Evolutionary history of life so others are not tempted to "re-arrange" it

Early signs of life


The details of the origin of life are unknown, though the broad principles have been established. It has been proposed that life, or at least organic components, may have arrived on Earth from space (see Panspermia), while others argue that terrestrial origins are more probable. The mechanisms by which life would initially arise are nevertheless held to be similar. The timing of the origin of life is highly speculative—perhaps it arose around four billion years ago. Somehow, in the energetic chemistry of early Earth, a molecule (or even something else) gained the ability to make copies of itself&mdash;the replicator. The nature of this molecule is unknown, its function having long since been superseded by life’s current replicator, DNA. In making copies of itself, the replicator did not always perform accurately; some copies contained an error. If the change destroyed the copying ability of the molecule, there could be no more copies, and the line would die out. On the other hand, a few rare changes might make the molecule replicate faster or better; those strains would become more numerous and successful. As choice raw materials (food) became depleted, strains which could exploit different materials, or perhaps halt the progress of other strains and steal their resources, became more numerous.

Several different models have been proposed explaining how a replicator might have developed. Different replicators have been posited, including organic chemicals such as modern proteins, nucleic acids, phospholipids, crystals, or even quantum systems. There is currently no method of determining which of these models, if any, closely fits the origin of life on Earth. One of the older theories, and one which has been worked out in some detail, will serve as an example of how this might occur.

The high energy from volcanoes, lightning, and ultraviolet radiation could help drive chemical reactions producing more complex molecules from simple compounds such as methane and ammonia. Among these were many of the relatively simple organic compounds that are the building blocks of life. As the amount of this “organic soup” increased, different molecules reacted with one another. Sometimes more complex molecules would result&mdash;perhaps clay provided a framework to collect and concentrate organic material. The presence of certain molecules could speed up a chemical reaction. All this continued for a very long time, with reactions occurring more or less at random, until by chance there arose a new molecule: the replicator. This had the bizarre property of promoting the chemical reactions which produced a copy of itself, and evolution began properly.

Other theories posit a different replicator. In any case, DNA took over the function of the replicator at some point; all known life (with the exception of some viruses and prions) use DNA as their replicator, in an almost identical manner (see genetic code). The first simple, sea dwelling organic structures appeared about 3,400 million years ago. It is considered that they may have formed when certain chemical (organic) molecules joined together. Prokaryotes, single-celled micro-organisms like blue green algae, were able to photosynthesize and produce oxygen. Around one thousand million years later, sufficient oxygen had built up in the atmosphere and hence it allowed multicellular organisms to proliferate in the Precambrian seas.

Evolution of life


Despite the uncertainty on how life began, it is clear that prokaryotes were the first organisms to inhabit Earth, approximately three to four billion years ago. No obvious changes in morphology or cellular organization occurred in these organisms over the next few billion years.

The eukaryotes were the next major innovation in evolution. These came from ancient bacteria being engulfed by the ancestors of eukaryotic cells, in a cooperative association called endosymbiosis. The engulfed bacteria and the host cell then underwent co-evolution, with the bacteria evolving into either mitochondria or hydrogenosomes. An independent second engulfment of cyanobacterial-like organisms led to the formation of chloroplasts in algae and plants.

As these early eukaryotes and prokaryotes were microscopic, most of the history of life describes simple microorganisms. It is only about a billion years ago in the Ediacaran period that complex multicellular organisms began to appear in the oceans. The evolution of multicellularity occurred in multiple independent events, in organisms as diverse as sponges, brown algae, cyanobacteria, slime moulds and myxobacteria.

Soon after the emergence of these first multicellular organisms, a remarkable amount of biological diversity appeared over approximately 10 million years, in an event called the Cambrian explosion. Here, the majority of types of modern animals evolved, as well as unique lineages that subsequently became extinct. Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis. About 500 million years ago, plants and fungi colonized the land, and were soon followed by arthropods and other animals. Amphibians first appeared around 300 million years ago, followed by early amniotes, then mammals around 200 million years ago and birds around 100 million years ago (both from "reptile"-like lineages). However, despite the evolution of these large animals, smaller organisms similar to the types that evolved early in this process continue to be highly successful and dominate the Earth, with the majority of both biomass and species being prokaryotes.

Life before Cambrian
The Precambrian extends from 4.6 billion years ago to the beginning of the Cambrian Period (about 570 Ma). It is not known when life originated, but carbon in 3.8 billion year old rocks from islands of western Greenland may be of organic origin. Well-preserved bacteria older than 3.46 billion years have been found in Western Australia. Probable fossils 100 million years older have been found in the same area. There is a fairly solid record of bacterial life throughout the remainder of the Precambrian.

The earliest cells had to form and exist in anoxic conditions. They were probably chemosynthetic. A quite diverse collection of soft-bodied forms is known from a variety of locations worldwide between and. These are referred to as Ediacaran or Vendian biota. Hard-shelled creatures appeared toward the end of that timespan.

A very diverse collection of animal forms appeared around, starting in the latest Precambrian with a poorly understood small shelly fauna and ending in the very early Cambrian with a very diverse, and quite modern Burgess fauna, the rapid radiation of forms called the Cambrian explosion of life.

Paleozoic life
The Paleozoic spanned from roughly 542 mya to roughly 251 mya (ICS 2004). The Paleozoic covers the time from the first appearance of abundant, hard-shelled animal fossils to the time when the continents were beginning to be dominated by large, relatively sophisticated reptiles and complex ferns and seed plants. The lower (oldest) boundary was classically set at the first appearance of creatures known as trilobites and archeocyathids. The upper (youngest) boundary is set at a major extinction event 300 million years later, known as the Permian extinction. Modern practice sets the older boundary at the first appearance of a distinctive trace fossil called Trichophycus pedum.

At the start of the era, animal life was confined to Ediacaran fauna. There is some evidence that simple life may already have invaded the land at the start of the Paleozoic, but substantial plants did not take to the land until the Ordovician, followed by animals in the Silurian. Neither group thrived on land until the Devonian. Although primitive vertebrates are known near the start of the Paleozoic, animal forms were dominated by invertebrates until the mid-Paleozoic. Fish populations exploded in the Devonian. During the late Paleozoic, great forests of primitive plants thrived on land forming the great coal beds of Europe and eastern North America. By the end of the era, the first large, sophisticated reptiles and the first modern plants (conifers) had developed.

Mesozoic life
The Mesozoic extended roughly from 251 Ma to 65 Ma (ICS 2004). The extinction of nearly all animal species at the end of the Permian period allowed for the radiation of many new lifeforms. In particular, the extinction of the large herbivorous and carnivorous dinocephalia left those ecological niches empty. Some were filled by the surviving cynodonts and dicynodonts, the latter of which subsequently became extinct. Animal life during the Mesozoic was dominated, however, by large archosaurian reptiles that appeared a few million years after the Permian extinction: dinosaurs, pterosaurs, and aquatic reptiles such as ichthyosaurs, plesiosaurs, and mosasaurs.

The climatic changes of the late Jurassic and Cretaceous provided for further adaptive radiation. The Jurassic was the height of archosaur diversity, and the first birds and placental mammals also appeared. Angiosperms radiated sometime in the early Cretaceous, first in the tropics, but the even temperature gradient allowed them to spread toward the poles throughout the period. By the end of the Cretaceous, angiosperms dominated tree floras in many areas, although some evidence suggests that biomass was still dominated by cycad and ferns until after the KT extinction.

Some have argued that insects diversified with angiosperms because insect anatomy, especially the mouth parts, seems particularly well-suited for flowering plants. However, all major insect mouth parts preceded angiosperms and insect diversification actually slowed when they arrived, so their anatomy originally must have been suited for some other purpose.

As the temperatures in the seas increased, the larger animals of the early Mesozoic gradually began to disappear while smaller animals of all kinds, including lizards, snakes, and perhaps the ancestor mammals to primates, evolved. The KT extinction exacerbated this trend. The large archosaurs became extinct, while birds and mammals thrived, as they do today.

Cenozoic life
The Cenozoic era covers the 65.5 million years since the Cretaceous–Tertiary extinction event. The Cenozoic is the age of new life. During this era, mammals diverged from a few small, simple, generalized forms into a diverse collection of terrestrial, marine, and flying animals. As the dinosaurs perished at the end of the Cretaceous period, the mammals took center stage. The mammals are the largest land animals of the Era, as the dinosaurs had been during the Mesozoic. The Cenozoic is just as much the age of savannas, or the age of co-dependent flowering plants and insects. Birds also evolved substantially in the Cenozoic.

Cambrian explosion
The Cambrian explosion (542–530 Ma) describes the profound diversification in life on Earth. Prior to around, organisms were on the whole simple, comprising of individual cells occasionally organised into colonies. Over the subsequent 70–80 million years, evolution would accelerate by an order of magnitude, and the diversity of life would begin to resemble today's. The fossil record provides us with a few cases of exceptional preservation around the end of this explosion, with famous units such as the Burgess shale offering a glimpse into a bustling yet strikingly different world, in stark contrast to the microbe-dominated seas of just 80 million years before.

The Cambrian explosion has generated extensive scientific debate. The seemingly rapid appearance of fossils in the "Primordial Strata" was noted as early as the mid 19th century; Charles Darwin saw it as one of the principal objections that could be lodged against his theory of evolution by natural selection.

The Cambrian explosion has proven difficult to study, partly because of the problems involved in matching up rocks of the same age across disparate continents. It should be borne in mind that absolute radiometric dates for much of the Cambrian, obtained by detailed analysis of radioactive elements contained within rocks, have only rather recently become available and that, especially for the Lower Cambrian, detailed biostratigraphic correlation&mdash;using widespread but short-lived species to match the ages of rocks&mdash;remains rather tenuous, particularly around the internationally-defined Precambrian/Cambrian boundary section in Newfoundland. Dating of important boundaries, and description of faunal successions, should thus be regarded with some degree of caution until better data become available.

Ordovician-Silurian extinction events
The extinctions occurred approximately 444–447 million years ago and mark the boundary between the Ordovician and the following Silurian Periods. During this extinction event, which may have been composed of several distinct closely spaced events, there were several marked changes in biologically responsive carbon and oxygen isotopes, which may indicate separate events or particular phases within one event.

At that time most complex multicellular organisms lived in the sea, and around 100 marine families became extinct, covering about 49 percent of genera of fauna (a more reliable estimate than species). The brachiopods and bryozoans were decimated, along with many of the trilobite, conodont and graptolite families.

Statistical analysis of marine losses at this time suggests that the decrease in diversity was caused more by a sharp increase in extinctions than by a decrease in speciation.

Late Devonian extinction
The Devonian extinction crisis primarily affected the marine community, and selectively affected shallow warm-water organisms rather than cool-water organisms. The most important group to be affected by this extinction event were the reef-builders of the great Devonian reef-systems, including the stromatoporoids, and the rugose and tabulate corals. The reef system collapse was so severe that major reef-building (effected by new families of carbonate-excreting organisms, the modern scleractinian corals) did not recover until the Mesozoic era.

The late Devonian crash in biodiversity was more drastic than the familiar extinction event that closed the Cretaceous: a recent survey (McGhee 1996) estimates that 22 percent of all the families of marine animals (largely invertebrates) were eliminated, the category of families offering a broad range of real structural diversity. Some 57 percent of the genera went extinct, and&mdash;the estimate most likely to be adjusted&mdash;at least 75 percent of the species did not survive into the following Carboniferous. The estimates of species loss depend on surveys of marine taxa that are perhaps not well enough known to assess their true rate of losses, and for the Devonian it is not easy to allow for possible effects of differential preservation and sampling biases. Amongst the severely affected marine groups were the brachiopods, trilobites, ammonites, conodonts, and acritarchs, as well as jawless fish, and all placoderms. Freshwater species, including our tetrapod ancestors, were less affected.

Permian-Triassic extinction event
The Permian-Triassic (P-Tr) extinction event, sometimes informally called the Great Dying, was an extinction event that occurred (mya), forming the boundary between the Permian and Triassic geologic periods. It was the Earth's most severe extinction event, with up to 96 percent of all marine species and 70 percent of terrestrial vertebrate species becoming extinct.

The extinction rate of marine organisms was catastrophic; it is harder to produce such detailed statistics for land, river, swamp and lake environments because good Permian-Triassic rock sequences from terrestrial environments are extremely rare (the Karoo basin is by far the best).

Even so, there is enough evidence to indicate that:
 * Over two-thirds of terrestrial amphibian, sauropsid ("reptile") and therapsid ("mammal-like reptile") families became extinct.
 * Large herbivores suffered the heaviest losses.
 * All Permian anapsid reptiles died out except the procolophonids (testudines have anapsid skulls but are most often thought to have evolved later, from diapsid ancestors).
 * The end-Permian is the only known mass extinction of insects. Many land plants became extinct, including groups which had been very abundant such as Cordaites (gymnosperms) and Glossopteris (seed ferns).

Triassic-Jurassic extinction event


The Triassic-Jurassic extinction event occurred 200 million years ago and is one of the major extinction events of the Phanerozoic eon, profoundly affecting life on land and in the oceans. Twenty percent of all marine families and all large Crurotarsi (non-dinosaurian archosaurs), some remaining therapsids, and many of the large amphibians were wiped out. At least half of the species now known to have been living on Earth at that time went extinct. This event opened an ecological niche allowing the dinosaurs to assume the dominant roles in the Jurassic period.

Cretaceous–Tertiary extinction event
The Cretaceous–Tertiary extinction event was the catastrophic mass extinction of extant animal species in a comparatively short period of time, approximately 65.5 million years ago.

Most, if not all, non-avian dinosaurs became extinct during or possibly a few years after the event. Non-avian dinosaur fossils are not found later than the K–T boundary, except for a few controversial exceptions. Many other groups of animals and plants, including mosasaurs, plesiosaurs, pterosaurs, and some invertebrates, also became extinct at the K–T boundary. The event marks the end of the Mesozoic Era, and the beginning of the Cenozoic Era.

Most of the extinctions occurred in a relatively short time because extensive weather changes reduced photosynthesis, thereby decreasing the amount of plant material available to herbivorous animals. This change in food supply caused a massive disruption in Earth's ecology.

Despite the severity of the K–T extinction event, there was significant variability in the rate of extinction of different classes of organisms. Organisms which depended on photosynthesis became extinct or suffered heavy losses due to reduced sunlight. Photosynthesizing organisms, from plankton (e.g. coccolithophorids) to land plants, formed the primary part of the food chain in the late Cretaceous. Herbivorous animals, which depended on plants and plankton as their food, died out as their food sources became scarce; consequently, top predators such as Tyrannosaurus rex also began dying. Animals which built calcium carbonate shells (for example, coccolithophorids along with many groups of molluscs, including ammonites, rudists, fresh water snails and mussels), as well as organisms whose food chain depended on these calcium carbonate shell builders, became extinct or suffered heavy losses. For example, it is thought that ammonites were the principal food of mosasaurs, a group of giant marine reptiles that became extinct at the boundary.

Most omnivores, insectivores and carrion-eaters appear to have survived quite well. At the end of the Cretaceous there seem to have been no purely herbivorous or carnivorous mammals. Many mammals, and the birds which survived the extinction, fed on insects, larvae, worms, snails, etc., which in turn fed on dead plant matter. They may have survived the collapse of plant-based food chains because they lived in "detritus-based" food chains.

In stream communities few groups of animals became extinct. Stream communities tend to rely less on food from living plants and more on detritus that washes in from land. This may have buffered them from extinction. Similar, but more complex patterns have been found in the oceans. Extinction was more severe among animals living in the water column, than among animals living on or in the sea floor. Animals in the water column are almost entirely dependent on primary production from living phytoplankton, while many animals living on or in the ocean floor feed on detritus or can switch to detritus feeding.

The largest air-breathing survivors, crocodilians and champsosaurs, were semi-aquatic. Modern crocodilians can live as scavengers and can survive for months without food. Modern crocodilian young are small, grow slowly, and feed largely on invertebrates and dead organisms or fragments of organisms for their first few years. This has been linked to crocodilian survival at the end of the Cretaceous.

Holocene extinction event
The Holocene extinction event is a name customarily given to the widespread, ongoing mass extinction of species during the modern Holocene epoch. The large number of extinctions span numerous families of plants and animals including mammals, birds, amphibians, reptiles and arthropods; a sizeable fraction of these extinctions are occurring in the rainforests. Because the rate of this extinction event appears to be much more rapid than the "Big Five" mass extinctions, it is also known as the Sixth Extinction. Since 1500 AD, 784 extinctions have been documented by the International Union for Conservation of Nature and Natural Resources. However, since most extinctions are likely to go undocumented, scientists estimate that during the last century, between 20,000 and two million species have become extinct, but the precise total cannot be determined more accurately within the limits of present knowledge. Up to 140,000 species per year (based on Species-area theory) may be the present rate of extinction based upon upper bound estimating.

In broad usage, the Holocene extinction event includes the notable disappearance of large mammals, known as megafauna, by the end of the last ice age 9,000 to 13,000 years ago. Such disappearances have been considered as either a response to climate change, a result of the proliferation of modern humans, or both. These extinctions, occurring near the Pleistocene / Holocene boundary, are sometimes referred to as the Pleistocene Extinction Event or Ice Age extinction event. However the Holocene extinction event continues through the events of the past several millennia and includes the present time.

The observed rate of extinction has accelerated dramatically in the last 50 years, to a pace greater than the rate seen during the Big Five. There is no general agreement on whether to consider more recent extinctions as a distinct event or merely part of a single escalating process. Only during these most recent parts of the extinction have plants also suffered large losses. Overall, the Holocene extinction event is most significantly characterised by the presence of man-made driving factors and its very short geological timescale (tens to thousands of years) compared to most other extinction events.

Significantly, the rate of species extinctions at present is estimated at 100 to 1000 times "background" or average extinction rates in the evolutionary time scale of planet Earth.

Prokaryote
It is generally accepted that the first living cells were some form of prokaryote and may have developed out of protobionts. Fossilized prokaryotes approximately 3.5 billion years old have been discovered, and prokaryotes are the most successful and abundant organism even today. In contrast the eukaryote only appeared between approximately 1.7 and 2.2 billion years ago. While Earth is the only known place in the universe where life exist, some have suggested structures within a Martian meteorite should be interpreted as fossil prokaryotes; this is open to considerable debate and skepticism.

Prokaryotes diversified greatly throughout their long existence. The metabolism of prokaryotes is far more varied than that of eukaryotes, leading to many highly distinct types of prokaryotes. For example, in addition to using photosynthesis or organic compounds for energy like eukaryotes do, prokaryotes may obtain energy from inorganic chemicals such as hydrogen sulfide.

Eukaryote
The origin of the eukaryotic cell was a milestone in the evolution of life, since they include all complex cells and almost all multi-cellular organisms. The timing of this series of events is hard to determine; Knoll (1992) suggests they developed approximately 1.6 to 2.1 billion years ago. Fossils that are clearly related to modern groups start appearing around 1.2 billion years ago, in the form of a red alga.

There are two main lineages within eukaryotes: unikonts, which include animals, fungi, the Amoebozoa, and choanoflagellates, and bikonts, which include the Rhizaria, Excavates, plants and relatives, Chromists, and Alveolates.

Eukaryotes became capable of photosynthesis when a cyanobacterium was engulfed by an ancestor to the Primoplantae (the group including green algae, red algae, and plants). Subsequently, green and red algae themselves became endosymbionts in a variety of eukaryote lines, a process which has happened multiple times.

The mitochondria of eukaryotes also derive from endosymbiosis and all eukaryotes have them, with the exception of a few groups (not related to each other) which instead have modified mitrochondria known as hydrogenosomes and mitosomes.

Archaea
The Archaea are a major group of microorganisms. Archaea are similar to other prokaryotes in most aspects of cell structure and metabolism. However, their genetic transcription and translation&mdash;the two central processes in molecular biology&mdash;do not show many typical bacterial features, and are in many aspects similar to those of eukaryotes. For instance, archaean translation uses eukaryotic-like initiation and elongation factors, and their transcription involves TATA Binding Proteins and TFIIB as in eukaryotes. Many archaeal tRNA and rRNA genes harbor unique archaeal introns which are neither like eukaryotic introns, nor like bacterial (type I and type II etc which can "home") introns.

Archaea were identified in 1977 by Carl Woese and George E. Fox as being a separate branch based on their separation from other prokaryotes on 16S rRNA phylogenetic trees. These two groups were originally named the Archaebacteria and Eubacteria, treated as kingdoms or subkingdoms, which Woese and Fox termed Urkingdoms. Woese argued that they represented fundamentally different branches of living things. He later renamed the groups Archaea and Bacteria to emphasize this, and argued that together with Eukarya they compose three Domains of living organisms.

The Archaea should not be confused with the geological term Archean eon, also known as the Archeozoic era. This refers to the primordial period of Earth history when Archaea and Bacteria were the only cellular organisms living on the planet. Probable fossils of these microbes have been dated to almost 3.5 billion years ago.