The History of Life

PRECAMBRIAN: Precambrian means: "before the Cambrian System." During the eighteenth century geologists began mapping the rock sequences of the earth's crust. They frequently found a basement complex made of igneous and metamorphic rocks beneath the lowest sedimentary layers. These were called the "Primitive" or "Primary", although the term "Primary Era' later came to be applied to the oldest sedimentary stage (later to be called the Paleozoic). In 1835 the English geologist Adam Sedgwick used the name "Cambrian" for the oldest sedimentary strata. Thereafter the underlying rocks were term Precambrian - "before the Cambrian". Thus, the Precambrian was originally defined as the era that predated the appearance of life in the Cambrian System. In the last few decades geologists have found that there are some hard-to-discern fossils in some Precambrian rocks, so this period was now also known as the Cryptozoic Eon or "hidden life" (from the words "crypt" = "hidden," and "zoon" = "life"). During the twentieth century the term "Cryptozoic" - age of hidden life" - was used to designate this period, whereas the Phanerozoic - "age of obvious (or revealed) life" - was used for those periods from which fossils of multicellular organisms are known (i.e. the Cambrian period to the present-day). Although the term latter term "Cryptozoic" is still in use by some geologist, it formally disappeared in favor of the older and well established term Precambrian. This old, but still common term has not a formal status in the subdivisions of the geological time scale; however, we still use the term Precambrian as it was originally used: to refer to the whole period of earth's history before the formation of the oldest rocks with recognizable fossils in them. The Precambrian covers almost 90% of the entire history of the Earth, from 4,500 to about 443 mya (million years ago). The Precambrian would be regarded as a first order division of the geological time scale, that is, an Eonothem; however, as stated above, it is not considered as a formal division of the geologic time scale. Instead the Precambiran time is divided into three major parts that are considered as first order divisions: the Priscoan Eonothem (also known as the Hadean), the Archean Eonothem and the Proterozoic Eonothem.

Division of the Precambrian based on Relative time: Chronostratigraphic Units

	Eonothem	Erathem	System
Precambrian	Proterozoic age of first life	Neoproterozoic	Upper 900	Ediacaran 650

		Mesoproterozoic	Middle 1600
		Paleoproterozoic	Lower 2500
	Archaean “first”, "primary" or ancient	Neoarchaean	Upper 2900
		Mesoarchaean	Middle 3300
		Paleoarchaean	Lower 3800
	Priscoan (Hadean): the time when the geosphere was still forming and life had not developed. Hadean referring to the hellish conditions of the very early Earth.

DOMAIN ARCHAEAN

Review the morphology of Archaea

Biological Features:

Methanothermus sp. Courtesy Karl Stetter.

It is believed that life on earth made its appearance in the seas during Archaean . The first life is believed to be the Eubacteria (i.e., bacteria prokaryotic organisms). The most accepted theory is that the Eubacteria are the ancestors of the members of the Domain Arachaea which includes organisms that can exist in extremely hostile environments such as thermal vents and hypersaline water. However, not all Archaeans are extremophiles , and, in fact, this domain is extremely diverse, and only recently being studied using genomic and proteomic methods. The earliest bacteria obtained energy through chemosynthesis (ingestion of organic molecules). They represent the oldest fossils that go back to about 3500 mya , and are known as bacterial microfossils. Archaeans are single-celled creatures that join bacteria to make up a category of life called the Prokaryotes (pro-carry-oats) . Prokaryotes' genetic material, or DNA, is not enclosed in a central cellular compartment called the nucleus. Bacteria and Archaea are the only prokaryotes. All other life forms are Eukaryotes (you-carry-oats) , creatures whose cells have nuclei. (Note: viruses are not considered true cells, so they don't fit into either of these categories.). However, while archaeans resemble bacteria and have some genes that are similar to bacterial genes, they also contain other genes that are more like what you'd find in eukaryotes. Furthermore, they have some genes that aren't like any found in anything else. View the difference between Prokaryots and Eukaryotes

The hypothesized process by which prokaryotes gave rise to the first eukaryotic cells is known as endosymbiosis <http://evolution.berkeley.edu/evolibrary/article/_0/endosymbiosis_03> The term was coined by Margulis: Lynn Margulis (born 1938) is a biologist and a professor at the University of Massachusetts Amherst. In 1967 she proposed a contentious new hypothesis which became her most important scientific contribution as the endosymbiotic theory of the origin of mitochondria as separate organisms that long ago entered a symbiotic relationship with eukaryotic cells through endosymbiosis. After the proposal of the endosymbiotic theory, Margulis predicted that if organelles were prokaryotic symbionts, then the organelles will have their own DNA that would be different from the DNA of the cell. This prediction was actually proven in the 1980's in mitochondria, centrioles, and chloroplasts.

These earliest fossils display what appear to be chemical signs of delicate chains of microbes that appear exactly like living blue-green algae (known as cyanobacteria ). For billions of years these bacteria formed extensive slimy carpets in shallow coastal waters, and before the end of Achaean about 2.5 bya they had also formed a thin crust on land. The structures that these bacteria formed are know as stromatolites, these accretionary growth structures produced by the prokaryotes, and also possibly Arachaeans and primitive Eukaryotes, became increasingly abundant during the Archaean, a fact of critical importance to the later evolution of life. However, an alternate hypothesis postulates that eukaryotes may have appeared in the late Archaea. Stromatolitic structures span the Precambrian and extend to modern time, though they are currently limited to several isolated environments.More information on Stramatolites <http://www.fossilmuseum.net/Tree_of_Life/Stromatolites.htm>

Geological Features:

The atmosphere that existed during Archean time would be toxic to most extant life on our planet. Also, rocks were just beginning to form at the crust of the earth. The atmosphere was very different from what we breathe today; at that time, it was likely a reducing atmosphere of methane, ammonia, and other gases which would be toxic to most life on our planet today. Also during this time, the Earth's crust cooled enough that rocks and continental plates began to form.

Paleontological Features:

Visit this site <http://www.ucmp.berkeley.edu/bacteria/bacteriafr.html> to gain an understanding of the Archaean biota.
The Archaea: have a diverse variety of shapes and exist not only as rods and dots (cocci) like bacteria but also as triangles, discs, plates and cup-shapes. Archaea was originally thought to be just like bacteria, but archaea is a much different and simpler form of life. It may also be the oldest form of life on Earth! Archaea are microbes. they were discovered in 1977 by Carl Woese and George Fox. Most live in extreme environments. These are called extremophyles. Archaea are a diverse and fascinating group of micro-organisms; however, some Archaea species are not extremophiles and live in ordinary temperatures and salinities. Some even live in your guts!

These Archaea species live in extreme heat near deep sea vents. Image courtesy of NOAA

When these microscopic organisms were first discovered (in 1977), they were considered bacteria. However, when their ribosomal RNA was sequenced, it became obvious that they bore no close relationship to the bacteria and were, in fact, more closely related to the eukaryotes (including ourselves!) For a time they were referred to as archaebacteria , but now to emphasize their distinctness, we call them Archaea .

They have also been called Extremophiles in recognition of the extreme environments in which they have been found:

thermophiles, which live at high temperatures;
hyperthermophiles, which live at really high temperatures (present record is 121°C!);
psychrophiles, which like it cold (one in the Antarctic grows best at 4°C);
halophiles, which live in very saline environments (like the Dead Sea);
acidophiles, which live at low pH (as low as pH 1 and who die at pH 7!);
alkaliphiles, which thrive at a high pH.

The >250 named species of Archaea are divided into 63 genera of which 24 are monotypic (meaning that there is only one species in the genus). The Archaea are divided into 3 main groups: (1) Euryarchaeota, (2) Crenarchaeota, and (3) Korarchaeota . The higher classification of the Archaea - as in many other taxa - is in dispute and the above groups may be called Kingdoms, Sections or Phyla depending on the source used. The Korarchaeota may contain the most ancient of living things and therefore are the closest thing we have to our original 'ancestral organism'.

The Euryarchaeota

There are four main types: (1) Methanogens (meth-an-oh-jins ) — archaeans that produce methane gas as a waste product of their "digestion," or process of making energy. (2) Halophiles ( hal -oh-files) — those archaeans that live in salty environments. (3) Thermophiles (ther -mo-files) — the archaeans that live at extremely hot temperatures. (4) Psychrophiles (sigh-crow-files)—those that live at unusually cold temperatures.

1. Methanogens

Nearly half (44.5%) of the known species of Archaea are unique in being capable of producing methane as part of their normal biochemical pathways. Organisms that produce methane are called methanogenic and the act of producing methane is called methanogenesis . These are found living in such anaerobic environments as the muck of swamps and marshes; the rumen of cattle (where they live on the hydrogen and CO₂ produced by other microbes living along with them); our colon (large intestine); sewage sludge ; the gut of termites.

They are chemoautotrophs ; using hydrogen as a source of electrons for reducing carbon dioxide to food and giving off methane ("marsh gas", CH₄) as a byproduct.

4H₂ + CO₂ -> CH₄ + 2H₂O

Methanogens are the most common and widely dispersed of the Archaea being found in anoxic sediments and swamps, lakes, marshes, paddy fields, landfills, hydrothermal vents and sewage works as well as in the rumen of cattle, sheep and camels, the cecae of horses and rabbits, the large intestine of dogs and humans, and in the hindgut of insects such as termites and cockroaches.

Two methanogens have had their complete genomes sequenced are:Methanococcusjannaschii and Methanobacteriumthermoautotrophicum

2. Halophiles

These are found in extremely saline environments such as the Great Salt Lake in the U.S. and the Dead Sea. They maintain osmotic balance with their surroundings by building up the solute concentration within their cells. This is a diverse group of organisms that live in extremely saline or salty environments, ie originally salt lakes but now also on the surfaces of highly salted foods such as fish and meats. These organisms are called extreme halophiles - this description means not only that they can live in highly saline environments but that they require a high concentration of salt in order to live at all. In practice, this means solutions with a minimum of 9% salt = 1.5M. Most species in this category prefer 12-23% salt solutions (2-4M) and can survive in saturate salt solutions ie 32% or 5.5M.

Naturally extremely saline environments suitable for organisms such as these are quite rare. They occur where sea water is trapped and allowed to evaporate; as the water level decreases so the salt concentration increases. All known extremely HalophilicArchaea stain gram negative, do not form resting stages or spores and reproduce by binary fission. There are 10 genera and 20 species of Extreme Halophiles, 5 of these genera are monotypic: Halobacterium; Halobaculum;Natrosobacterium; Natrialba;Natrosomonas. The other genera are: Natrarococcus(2 species); Haloarcula (2 species); Halococcus (2 species); Haloferax (4 species); Halorubrum (5 species).

3. Thermoacidophiles

As their name suggests, these like it hot and acid (but not as hot some of the Crenarchaeota!). They are found in such places as acidic sulfur springs (e.g., in YellowstoneNational Park) and undersea vents ("black smokers"). As they name suggests this small group of the Euryarchaeota are organisms that specialize in living in extremely hot environments such as hydrothermal vents on the sea bed and in hot springs. The five key genera in this group are Thermococcus,Pyrococcus,Methanopyrus,Archaeoglobus and Ferroglobus. Though living in hot water is not that unusual for prokaryotes the organisms in this group are all hyperthermophiles and have an optimum living temperature of 80(C or greater. Methanopyrus is a rod-shaped methanogenic organism found in hydrothermal vents. Thermococcus and Pyrococcus (literally 'fireball') are both obligate anaerobic chemoorganotrophs which means that they live on organic molecules in environments where there is no oxygen. Thermococcus lives at 70-95(C, whilst Pyrococcus lives at temperatures from 70-100(C. Note that under pressure, ie underground or deep in the sea, water can remain liquid at temperatures greater than 100C because the boiling point of any liquid is dependent on pressure.

The Crenarchaeota

The Crenarchaeota are a smaller group than the Euryarchaeota which contains the majority of the known Archaea. The Crenarchaeota are primarily found in extreme environments either hot ones or cold ones. Little is known about the cold adapted species except that they live in considerable numbers - 104 per ml. They are found in the Antarctic and probably the Arctic as well. The first members of this group to be discovered like it really hot and so are called hyperthermophiles. One can grow at 121°C (the same temperature in the autoclaves used to sterilize culture media, surgical instruments, etc.).

Many like it acid as well as hot and live in acidic sulfur springs at a pH as low as 1 (the equivalent of dilute sulfuric acid). These use hydrogen as a source of electrons to reduce sulfur in order to get the energy they need to synthesize their food (from CO₂).

One member of the group, Aeropyrum pernix, has had its genome completely sequenced.

Other members of this group seem to make up a large fraction of the plankton in cool, marine waters; the microbes in soil that convert ammonia into nitrites (nitrification ).

Evolutionary Position of the Archaea

The archaea have a curious mix of traits characteristic of bacteria as well as traits found in eukaryotes. Some extremophile species love the heat! They like to live in boiling water, like the geysers of YellowstonePark, and inside volcanoes. They like the heat so much that it has earned the nickname "thermophile", which means "loving heat", and it would probably freeze to death at ordinary room temperature. Other extremophileArchaea love to live in very salty, called hypersaline, environments. They are able to survive in these extreme places where other organisms cannot. These salt-loving Archaea are called halophyles.

Archaea requires neither sunlight for photosynthesis as do plants, nor oxygen. Archaea absorbs CO₂, N₂, or H₂S and gives off methane gas as a waste product the same way humans breathe in oxygen and breathe out carbon dioxide.

Planets which contain an environment wherein archaea might survive include Venus, the past environment of Mars, Jupiter, Saturn , and Jupiter's moon Io .

Thermophiles and biotechnology: the Termus aquaticus case
An emerging new fieled of applied reserach has developed in the last decade, that is biotechnology. The use heat resistant microbe to unravel the way on how to copy DNA and amplify it using the polymerase chain reaction (PCR). This type of research finds wide use in medical diagnosis (AIDS, for instance) and forensics (DNA fingerprinting) and has become the basis of a $300,000,000 industry. So the Yellowstone Park that had been justly famous for its wildlife, it is now becoming famous for the incredibly small, amazingly versatile microbes that are found in such profusion here, and which are so rare elsewhere.

Important events in the history of life:

4.6 bya: Origin of Earth

3.5 bya: Prokaryoteds (bacteria dominate)

2.5 bya: Free oxygen accumulates in the atmosphere

1.5 bya: Eukaryotes: First nucleated cell

0.5 bya: Cambrian Explosion. First multicelular eukaryotes

VENDIAN also known as the Ediacaran System:

The oldest fossils within KingdonAnimalia are Vendian-age 650 to 544 mya, are found at nearly 30 localaities around the world. The Ediacara Hills of Southern Australia, and the White Sea Region of Northern Russia are two of the more famous. The Ediaracan fossils where first discovered in 1946. They are regarded as 700 million years old it is the oldest fossil lagerstätte, named Ediacaran geological system. The preserved soft-bodied organisms, including similar forms now found worldwide are collectively referred to as Ediacaran biota. The Ediacaranis now a System in its own right, the first to be added to the Geological Time Scale in 120 years. It extends from around 600 m.y. (the actual date has yet to be determined) to the beginning of the Cambrian at 542 m.y. The International Commission of Stratigraphy, part of the International Union of Geological Scientists, made the decision in July of 2004.

On the taxonomic status of Ediacaran Fossils: The Vendobionta
Ediacaran fossils were first discovered in the Flinders Range, South Australia in coarse sandstones lying beneath rocks with the first shelly fossils of Early Cambrian age. These are large, flat and carpet-like fossils. The initial work indicated that they were metazoans; that is, true animals -- medusoids, sea pens and annelid worms, possibly even arthropods and echinoderms -- and that they were soft-bodied precursors to animal groups found in Cambrian rocks. This traditional view was challenged by Dolf Seilacher, an iconoclastic German academic paleontologist, who declared that the Ediacaran fossils were not animals because none shows any evidence of having organs, muscles, mouth, anus, gut or legs. Instead he interpreted the Ediacarans as unique quilted and immobile organisms constructed as a series of fluid- or jelly-filled cells -- like air-mattresses -- that must have absorbed sunlight and nutrients directly from seawater through their skin. Seilacher suggested that these fossils represent a new kingdom of organisms called Vendobionta that became extinct before the beginning of the Cambrian.

Typically, the Vendian or Ediacaran fossils are preserved as thin impressions on bedding surfaces of fine to medium-grained sedimentary rocks. Ostensibly, these organisms were very thin, lacked any mineralized hard parts or well developed organs or organ systems, and had a quilt-like outer surface. Some uncertainty exists as to what groups of animals these fossils might represent, and, in fact, if they were ancestral to the multicellular organisms that appeared later in the Cambrian. The so-called Tommotian fauna (biota) appear near the end of the Proterozoic, immediately preceding the Cambrian explosion. These small shelly animals were a prelude to the metazoans with hard exoskeletons that would rapidly diversify in the Cambrian.

Taken from: Ediacara Biota, ancestors of Modern Life or evolutionary dead end <http://geol.queensu.ca/museum/exhibits/ediac/ediac.html>

Eonothem	Erathem	System	When began My ago	duration My
Proterozoic	Neoproterozoic 1000 mya	Ediacaran	600	58
		Cryogenian	850	250
		Tonian	1000	150
	Mesoproterozoic 1600myra	Stenian	1200	200
		Ectasian	1400	200
		Calymmian	1600	200
	Paleoproterozoic 2500 myra	Statherian	1800	200
		Orosirian	2050	250
		Rhyacian	2300	250
		Siderian	2500	200

This chart is modified from the International Commission on Stratigraphy

Notes on the Classification of Organisms
Organismal diversity is the product of evolution.
Evolutionary paths are branched and numerous, though most arrive at dead ends with organisms which do not survive environmental change. We will consider these evolutionary paths (called lineages), and the processes that carry organisms along them.
While the lineage of any given organism may have twisted repeatedly according to the whims of chance and change, key nodes may nevertheless be tracked retrospectively. These nodes consist of times of identifiable change, particularly points of divergence between two lineages (speciation events). The delineation of these nodes in organismal lineages is accomplished through fossil reconstruction of the past as well as by comparing extant organisms, looking for similarities and differences in anatomies, physiologies, genes, behaviors, etc. From this information classification and phylogenetic reconstruction is accomplished.
In this lecture we will review the general way on how organisms are systematically classified, in addition we will attempt to compare how the classification of living organisms compares with that of fossils forms.

Some basic rules for the classification of organisms:
In order to make sense of the diversity of organisms, it is necessary to group similar organisms together and organize these groups in a non-overlapping hierarchical arrangement.

Taxonomy is the science of biological classification.
The basic taxonomic group is the species, which is defined in terms of either sexual reproduction or general similarity.
Morphological, physiological, metabolic, ecological, genetic, and molecular characteristics are all useful in taxonomy because they reflect the organization and activity of the genome. Nucleic acid structure is probably the best indicator of relatedness because nucleic acids are either the genetic material itself or the products of gene transcription.

Classifications are based on any analysis of possible evolutionary relationships (phylogenetic or phyletic classification) or on overall similarity (phenetic classification).

Linnaeus, Carolus (late 1700s) system of classification according to similarity: Carolus Linnaeus developed a system of classification of every known organism up to that time. This system is based on creating and differentiating groups in terms of structural (and other) similarities and differences. Linnaeus also invented binomial nomenclature to keep track of group members. That is the use of Genus and species names for all the organisms, e.g. Home sapiens for humans.

Systematics
Systematics is the study of the diversity of organisms and their evolutionary relationships.
Science of classification: Systematics is the science of the classification of organisms. The main goal of systematics is the discovery and codification of phylogenetic relationships between organisms.

The term systematics often is used for taxonomy. However, many taxonomists define it in more general terms as 'the scientific study of organisms with the ultimate object of characterizing and arranging them in an orderly manner.' Any study of the nature of organisms, when the knowledge gained is used in taxonomy, is a part of systematics. Thus systematics encompasses disciplines such as morphology, ecology, epidemiology, biochemistry, molecular biology, and physiology.

Taxon (pl. taxa), A taxon is a phylogenetic grouping of organisms. There are two related processes in taxonomy. Taxonomy is the science concerned with the identification, classification, nomenclature of organisms.

Taxonomy [Greek taxis, arrangement or order, and nomos, law, or nemein, to distribute or govern] is defined as the science of biological classification. In a broader sense it consists of three separate but interrelated parts: classification, nomenclature, and identification.
Note that the terms systematics and taxonomy can often be used semantically in a nearly indistinguishable manner.

Identification is the practical side of taxonomy, the process of determining that a particular (organism) belongs to a recognized taxon.

Classification is the arrangement of organisms into groups or taxa.

Nomenclature is the branch of taxonomy concerned with the assignment of names to taxonomic groups in agreement with published rules.
Note that ideally names have taxonimic meaning, i.e., they give clues to phylogenetic relationships.

Hierarchical classification The full description of a given organism's place among all the world's organisms does not end with its binomial designation. There exists a hierarchy of designations only the last of which describe genera and species denomination. A category in any rank unites groups in the level below it based on shared properties. The major designations, listed in terms of increasing specificity, include:

domain (empire/super-kingdom)
    kingdom
        phylum
            class
                order
                    family
                        genus
                            species

Phylogeny [phylogenetic group]
A phylogeny is a representation of organisms based on and describing evolutionary relationships.

Monophyletic
A phylogenitic group (i.e., taxon) all of whose members are descended from a common ancestor which is a member of the same phylogenitic group, and which consists of all of the (known or considered) descendants of that common ancestor.
A monophyletic taxon is a good taxon in an evolutionary sense, meaning that no members which ought to be a part of the taxon, in terms of ancestor-descendant relationships, are excluded.

Symbolic examples:
For example, if both B and C are descendants of A, then a monophyletic taxon would consist of all three species.
For example, if both C and D are descendants of B, and B is a direct descendant of A, then a monophyletic taxon of these species could consist either of all four species, or of just species B, C, and D.

Polyphyletic
A phylogenitic group (i.e., taxon) all of whose members are descended from a common ancestor, but in which one or more common ancestor is not a member of the same phylogenitic group, and that missing common ancestor is the most recent common ancestor.

Paraphyletic (Missing member)
A phylogenitic group (i.e., taxon) all of whose members are descended from a common ancestor, but which does not include all of the known or considered descendants of that common ancestor. In the usage of cladists, a paraphyletic taxon is a monophyletic taxon in which a member, other than the most recent common ancestor, is excluded. Typically paraphyletic taxa represent the improper exclusion of members on the basis of phenotypic differences rather than on the basis of ancestor-descendant relationships.

Clades
The purpose of phylogenetic studies is to establish the evolutionary relationships among different species. In particular, we are interested in the identification of natural clades. A clade is defined as a group of species that share a common ancestor, which is not shared by another species outside of the clade.
Monophylectic taxon:
In other words, a clade is a monophyletic taxon.
Clades are the only phylogenetically/evolutionarily real taxons.
Other, non-monophyletic (e.g., paraphyletic) taxons are based on, for example, just morphological similarities rather than evolutionary relationships.

Example: reptiles do not form a natural clade:
The reptiles do not represent a true clade because, while there may be strong evolutionary relationships within this group, there are also a number of taxa which evolved from within this taxa but which are not included in the taxa reptiles
Examples of these latter taxa include the birds, the mammals, and the dinosaurs as well as a number of extinct lineages.

Example: apes + humans form a clade:
The designation apes, like reptiles, does not form a true clade, though here this problem is easily corrected simply by accepting that humans are modified apes (just as apes are modified mammals and mammals are modified reptiles and reptiles are modified amphibians and amphibians are modified fish, etc.). That is, humans plus those animals typically classified as apes together form a monophyletic taxon, i.e., a clade.