Evolution
A support site for modules SC0060-3 Evolution
and SCM009-M Molecular Evolution
Page last updated 11/02/02

Early evolution
[required for SC0060-3 only]

The fundamental molecular/cellular developments of life all occurred in the achean and proterozoic eons,
that between them account for ca.75% of Earth's history. These early events are listed in the table below.
'mya' = million years ago.
 

The diagram below shows the eons and periods of Earth's history. Note that the current phanerozoic eon, where most
evolutionary knowledge and study is focussed, and is split into periods, accounts for only ca.13% of Earth's history.
The row heights are in approximate proporation to the time.
 

eon	era	period	events	mya
priscoan or solar or hadean			formation of Solar System and Earth; intense comet/asteroid bombardment	4600 - 4000
archaean			Earth's surface <100oC ca.3800 mya; prebiotic evolution - origin of life; bacteria / archaea split; first fossil cell ca.3465 mya; oxygenic photosynthesis; aerobic respiration	4000 - 2500
proterozoic	paleoproterozoic		oxygen revolution; eukarya ca.2000 mya; mitochondria 2000-1500 mya; sex	2500-1600
	mesoproterozoic		protist radiation; protist / other eukarya split ca.1230 mya; chloroplasts ca.1000 mya; plant / fungi / animal split ca.1000 mya	1600-1000
	neoproterozoic	( vendian )	multicellularity; body plan development mechanisms ( earliest multicellular animals - basic body plans emerge )	1000-590 ( 650-550 )
phanerozoic	paleozoic	cambrian	cambrian explosion of all eukarya phyla except chordata	590 - 505
		ordovician	chordata; end ordovician extinction (60%)	505 - 438
		silurian	jawed fishes; terrestrial vascular plants & arthropods	438 - 408
		devonian	amphibians; insects	408 - 360
		carboniferous	radiation of vascular plants (coal deposits formed); reptiles; winged insects	360 - 286
		permian	radiation of reptilia; radiation of winged insects; end permian extinction (90%)	286 - 248
	mesozoic	triassic	dinosaurs; flowering plants; birds; monotremes	248 - 213
		jurassic	radiation of dinosaurs / marine / flying reptiles; spread of gymnosperms	213 - 144
		cretaceous	marsupials & eutherians; KT extinction (50%)	144 - 65
	cenozoic	tertiary	eutherian radiation; angiosperm radiation	65-2
		quaternary	Homo	2-0

The phanerozoic eon produced almost all of the fossil record, since fossils are very rarely formed anyway, and then usually
require hard body parts (exo & endo skeletons, shells, etc) which have only been a feature of life in this eon. Prior to this eon
(ie, before 590 mya) is often dismissed as the 'Precambrian' and produced few fossils.

Molecular phylogenetics (tracing evolutionary relationships and kinship) via comparison of rRNA sequences (which change
very slowly and so allow ancient events to be studied), together with fresh biochemical insights and geological data,
can shed light on the crucial early events of evolution, although the picture is often quite difficult to interpret.

rRNA sequence analysis and comparison of molecular/cellular properties show there to be three overall domains of life;
bacteria, archaea, and eukarya. Life was first feasible once the Earth's surface temperature fell below 100oC, which was
ca. 3,800 mya - although some prebiotic evolution may pre-date this. Modern extremophiles can withstand such high
temperatures. Analysis of relative levels of carbon isotopes in ca.3,800 mya rocks in Greenland does suggest that life
existed as early as 3,800 mya.

The first fossil cells are ca. 3500 mya, and seem apparently to be cyanobacteria or similar, which may suggest that
photosynthesis of some description occurred back then. It thus appears that the divergence between archaea and bacteria
was at or before ca.3500 mya, and so the molecular/cellular properties shared in common by these domains are likely
to pre-date this. Such properties (see table) include single naked DNA chromosomes (so genes are replicated in unison),
operons (so genes expressed in unison), the universal genetic code, and the essential basis of the protein synthesis
machinery (ie, ribosomes).
 

	archaea	eukarya	bacteria
chromosomes	Y	Y	Y
operons	Y	N	Y
universal genetic code	Y	Y	Y
protein synthesis at ribosomes	Y	Y	Y
initiator amino acid = met	Y	Y	N
ribosomes inhibited by antibiotics	N	N	Y
introns	Y/N	Y	N
>1 RNA polymerase	Y	Y	N
nuclear envelope	N	Y	N
membraneous organelles	N	Y	N
petidoglycan cell wall	N	N	Y
some branched fatty acids in cell membrane	Y	N	N

There are clear molecular/cellular distinctions between archaea and bacteria, and these must have occurred after the divergence
between these, but before eukarya arose ca.2000 mya. Such properties (see table) include protein synthesis initiator being
methionine in archaea and formyl-methionine in bacteria, bacterial ribosomes being suseptible to inhibition by antibiotics but
archaeal not, there being multiple RNA polymerases in archaea but just one in bacteria, bacteria having a peptidoglycan cell wall
but archaea not, and there being some branched fatty acids in archaeal cell membranes but none in bacteria cell memranes.

Eukarya share all of the above properties (except branched fatty acids in the cell membrane) with archaea (see table),
and so seem to have diverged from archaea at ca. 2000 mya (see tree).

The origins of introns are unclear. These are the norm in eukarya, are sometimes seen in archaea, and never seen in bacteria.
The 'introns early' theory suggests introns were a feature of early cells but were lost in bacteria to increase efficiency.
The 'introns late' theory suggests that introns arose in archaeal ancestors of eukarya, and then developed in eukarya
to facilitate easy recombination of protein domains (a phenomenon known as exon shuffling) to produce new proteins.

Overall though, the above is probably too simplistic - bacterial sequences can be detected in eukarya genomes for example.
This could have happened via horizontal gene transfer, making the overall picture complicated.

Although eukarya share several aspects with archaea (and not bacteria), there are molecular/cellular features unique to eukarya,
which include (see table) the nucleus, plastids (ie, mitochondria and chloroplasts), endomembrane system (ie, endoplasmic
reticulum and Golgi apparatus), cytoskeleton, 9+2 flagella (where present), multiple linear chromosomes comprising DNA
complexed with histone proteins (naked single circular DNA genome with no histones in archaea and bacteria), and sex.

The origin of the nuclear envelope is unclear. Suggestions include derivation from the archaeal cell membrane (along with the
endomembrane system), or that an archaean cell which became the nucleus was engulfed by a gram negative bacterial cell
which became the surrounding eukaryal cell, the genome being expelled from the latter.

Plastids are enclosed by a double membrane, the inner of which has a number of proteins that resemble bacterial cell
membrane proteins, and are of similar size to bacterial cells. Plastids have their own small naked circular DNA genome
(no histones) and the protein synthesis machiner (ribosomes) resemble those in bacteria (are suseptible to inhibition by
antibiotics, the protein synthesis initiator is formyl-met, promoters are of the bacterial type,and there are no introns).

Plastids thus seem derived from bacteria, and this is confirmed now by molecular phylogeny using comparisons of
very slowly changing rRNA sequences. Mitochondria seem to have arisen from alpha-proteobacteria ca.2000-1500 mya
and chloroplasts from cyanobacteria ca.1000 mya. The idea is therefore that plastids are endosymbionts, ie, were once
bacterial cells that were engulfed by ancestral eukarya cells so that the latter gained aerobic respiration / oxygenic
photosynthesis capacity whilst the former gained a reliable plentiful supply of carbon sources. There are some plastid
genes in the nuclear genome that probably transferred across, but less so with chloroplasts perhaps confirming their
more recent origin. Transfer of plastid genes to the nucleus would be beneficial to avoid conflicts with sex and/or to
allow repair of these genes by the nuclear repair mechanisms.

Other features of eukarya may be of endosymbiotic origin, eg, 9+2 flagella are microtubule extensions of cytosol
and cell membrane (rather than naked protein as in bacteria) and could have once been spirochete bacteria,
peroxisomes might once have been gram positive bacteria. However, the evidence here is rather thin - for instance
the fact that these features have no genome - perhaps it has been lost?, maybe plastids only retain genes for
proteins that are difficult to transport across the double membrane?

Note the four modes of nutrition (see table) below. ATP is the universal energy currency of
all cells and the glycolysis pathway (which does not require oxygen) is present in all cells,
and so these must both have arisen very early (probably before ca.3500 mya).
 

	chemotrophy	phototrophy
autotrophy	chemoautotrophs: obtain energy from oxidation of inorganic compounds like hydrogen sulphide, ammonia and ferrous compounds, and obtain carbon from CO2, eg, certain prokaryotes like sulpholobus	photoautotrophs: 'photosynthesis' - obtain energy (ATP and reducing power generation) from light, and obtain carbon from CO2, eg, cyanobacteria, some protists, plants	use carbon dioxide (CO2) as sole carbon source
heterotrophy	chemoheterotrophs: obtain energy from oxidation of organic molecules, which also act as carbon sources, eg, certain prokaryotes, certain protists, fungi, animals	photoheterotrophs: obtain energy (ATP generation) from light but obtain carbon from organic molecules, eg, certain prokaryotes	use at least one organic molecule as carbon source
	utilise chemical energy obtained from the environment	utilise solar light energy

The first cells were probably chemoautotrophs (see diagram) synthesising ATP by oxidation of hydrogen sulphide and
iron (II) compounds then abundant in the environment. The released energy could have been harnessed via production
of a proton gradient, stimulating evolution of electron transport chains, and the reducing equivalents (electrons)
generated used in carbon dioxide fixation and thence biosynthesis. There may also have been opportunistic absorption
of abiotically produced organic compounds from the environment (ie, chemoheterotrophy), although these were not
present in sufficient quantity to make anything more than a small contribution.

Early cells may have used membrane pigments to protect themselves from the then intensive UV. The excitation of
these pigments could become coupled to proton pumping and the resultant gradient used to drive ATP synthesis.
Bacteriorhodopsin does this in some modern bacteria. Modern proteobacteria split hydrogen sulphide to provide
electrons for this process, and this probably pre-dates oxygenic photosynthesis. However, water is obviously very
abundant so there would have selection pressure to split water and so release oxygen.

Initially, oxygen released by photosynthesis was absorbed by iron (II), then abundant in the sea, thus oxidising it to
insoluble iron (III) oxide (ie, rust!). Red 'banded iron deposits'of iron (III) oxide are marked in marine sediments of ca.2500 mya.
Once most/all iron (II) had been oxidised to iron (III), then oxygen appeared in, and began to increase in, the atmosphere,
gradually building up from zero ca.2000 mya to approximately present levels ca. 500 mya. This was the "oxygen revolution".

Oxygen is corrosive, so prokaryotic life then either became extinct, or survived in anaerobic (oxygen free) environments
(and do so to this day), or evolved antioxidant protective mechanisms. The latter could begin to use oxygen to pull
electrons from organic molecules, leading to aerobic respiration. The respiratory electron transport chain probably
evolved from established photosynthetic electron transport, and the citric acid cycle probably evolved using steps from
several biosynthetic pathways (it still has key links to biosynthesis today).

Multicellularity arose 1000-700 mya, and, molecular phylogeny from rRNA sequences confirms this.
The advent of multicellularity produced plants, fungi and animals from various protists (probably the
green alga charophytes, aquatic saprobe chytrids, and colonial flagellate choanoflagellates respectively).
Experimentally, green algae cultured with a predator live and stably reproduce as an 8-cell cluster after
ca.100 generations. This 8-cell size is such that they are too large to be predated but small enough for
each cell to obtain nutrients from the medium. Note all 8 cells are derived by division from 1 cell so there
is genetic identity and no genomic conflict - the same being true for multicellular organisms today.

However, the 8-cell clusters have no differentiation, which requires gene regulation (so some genes can be
expressed in some cell types but not in others) and epigenetic inheritance (some kind of way of passing on
cellular properties in cell division in addition to normal DNA heredity - so that cells can maintain their
differentiated state but still divide when required. However, it has been shown that gene expression can
change with time in prokaryotes, and also some of the mechanisms used for epigenetic inheritance in
multicellular organisms (eg, DNA methylation of genes) have been seen in prokaryotes - and so it seems
differentiation need not have been a such a massive step for the early eukarya.

Multicellularity allows sex (requires differentiation of cells into germ-line and soma) and large complex organisms
(so selection can operate at a range of levels - gene, cell, individual, and population). The latter requires
developmental mechanisms, but it's notable that the seemingly diverse animal phyla are all based on a
relatively limited basic body plan determined by a surprisingly small number of genes (eg, the Hox complex).

Almost all animal phyla arose in the "Cambrian explosion" 590-505 mya, possibly driven by oxygen levels
becoming such that aerobic respiration could meet the energy demand of animal locomotion, feeding, etc.

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