Biodiversity:

The Geologic Record:

Relative Period Epoch Age Important events

duration (millions
of Eons of years
and Eras: ago)
Archaean Approx.4 Origin of Earth.
600

3800 Oldest known rock on earth’s

surface.
3500 Oldest fossils of
cells(prokaryotes).
2700 Concentration of atmospheric
O2 begins to increase.
Proteroz 2200 Oldest fossils of eukaryotic
oic cells.
600 Diverse algae and soft-bodied
invertebrate animals.
Phaneroz
oic: Cambrian 488-5542 Sudden increase in diversity
Paleozoic of many animal phyla
(Cambrian explosion).
Ordovicia 443.7- Marine algae abundant;
n 488 colonisaton of land by plants
and arthropods.
Silurian 416-443 Diversificaton of early
vascular plants.
Devonian 359.2- Diversification of bony fishes;
416 first tetrapods and insects.

Carbonife 299-359 Extensive forests of vascular

rous plants; first seed plants;
origin of reptiles; amphibians
dominant.

Permian 251-299 Radiation of reptiles; origin of

most present-day orders of
insects; extinction of many
marine and terrestrial life at
the end of period.

Mesozoic Triassic 199.6- Cone-bearing plants dominate

299 landscape; radiation of
dinasaurs; origin of mammal-
like reptiles.
 Jurassic 145.5- Gymnosperms continue as
199 dominant plants; dinasaurs
abundant and diverse.

Cretaceou 65.5-145 Flowering plants appear;

s many groups of organisms
become extinct at the end of
period(Cretaceous
extniction).

Cenozoic Paleogene Paleoce 55.8-65 Major radiation of mammals,

ne birds, and pollinating insects.
Eocene 33.9- Angiosperm dominance
55.8 increase; continued radiation
of most modern mammalian
orders.

Oligoce 23-33.9 Origin of many primate

ne groups, including apes.

Neogene Miocene 5.3-23 Continued radiation of

mammals and angiosperms;
ape-like ancestors of humans
appear.

Pliocene 1.8-5.3 Origin of genus Homo.

Pleistoc 0.01-1.8 Ice ages; humans appear.

ene
Holocen Now-0.01 Historacal time.
e

As prokaryotes evolved, they exploited and changed young Earth. The

oldest known fossils, dating from 3.5 bilion years ago, are fossils of
stromatolites, which are rock-like structures composed of many layers of
bacteria and sediment. Present-day stromatolites are found in a few
warm, shallow, salty bays. If bacterial communities so complex existed 3.5
bilion years ago, it is a reasonable hypothesis that life originated much
earlier, perhaps as early as 3.9 bilion years ago, when earth began to cool
to a temperature at which liquid water could exist. It is clear that
prokaryotic life was already flourishing when earth was still relatively
young. Fairly early in prokaryotic history, two main evolutionary branches,
the bacteria and the archaea, diverged. The first prokaryotes were
probably the autotrophs and the heterotroph, and they were earth’s sole
inhabitants from at least 3.5 to about 2 bilion years ago. These organisms
transformed the biosphere of our planet. The chemiosmotic machanism of
ATP synthesis, in which a complex set of membrane-bound proteins pass
electrons to reducible electron acceptors with the generation of ATP from
ADP, is common to all three domain of life-bacteria, archaea, and eukarya.
There is strong evidence that this electron transport machanism actually
originated in organisms that lived before the last common ancestor of all
present-day life. The earliest of these electron transport systems likely
evolved before there was any free oxygen in the environment and before
the appearance of photosynthesis; the organisms that used it would have
required a plentiful supply of energy rich compounds such as hydrogen,
methane, and hydrogen sulfide. The earliest types of photosynthesis did
not produce oxygen. Oxygenic photosynthesis probably evolved about 3.5
bilion years ago in cyanobacteria. The accumulation of oxygen in the
atmosphere about 2.7 bilion years ago posed a challenge for life, but it
also selected for certain adaptation such as cellular respiration using
oxygen.

Eukaryotic cells arose from symbioses and genetic exchanges between

prokaryotes. The oldest fossils that most researchers agree are eukaryotic
are about 2.1 bilion years old. Other fossils, of corkscrew-shaped
organisms that resembled simple, single-celled algae, are slightly
older(2.2 bilion years), but their eukaryotic nature is less certain.
However, some researchers postulate a much earlier eukaryotic origin
based on traces of molecules similar to cholesterol found in rocks dating
back 2.7 bilion years. Such molecules are made only by eukaryotics cells
that can respire aerobically. If confirmed, these finding could mean that
eukaryotes evolved when the oxygen revolution was beginning to
transform Earth’s environments dramatically. Prokaryotes lack many
internal structures, such as the nuclear envelope, endoplasmic reticulum,
mitochondrion, and glogi apparatus. How did the more complex
organisation of the eukaryotic cell evolve from the simpler prokaryotic
condition? A process called endosymbiosis probably led to mitochondria
and plastids. Mitochondria and plastids likely evolved from prokaryotes
that were ingested by and lived symbiotically within larger cells. The
strong evidence for this hypothesis is that the researchers found that the
alpha proteobacteria are the closest relatives of mitochondria, and that
cyanobacteria are the closest relatives of plastids, genetically.

Early classification systems had two kingdoms: plants and animals. A

system that was proposed later had five kingdoms: monera, protoctista,
plantae, fungi, and animalia. A three-domain system( bacteria, archaea,
and eukarya) has replaced the five kingdom-system.

Monera:
 Prokaryotes

Eukaryotes

Protoctista:

Plantae: Fungi: Animalia

:

Five-kingdom system:

Domain Domain Domain

Universal

Three-domain system:

Prokaryotes:
Structural, functional, and genetic adaptation contribute to prokaryotic
success. Most prokaryotes are unicellular, although some species
aggregate transiently or permanently in colonies. Prokaryotic cells
typically have diameters in the range of 1-5 µm, much smaller than the 10-
100 µm diameter of many eukaryotic cells. One of the most important
features of nearly all prokaryotic cells is their cell wall, which maintains
cell shape, provides physical protection, and prevents the cell from
bursting in a hypotonic environment. In a hypertonic environment, most
prokaryotes lose water and shrink away from their wall (plasmolyse), like
other walled cells. Severe water loss inhibits the reproduction of
prokaryotes, which explain why salt can be used to preserve certain foods.
The cell walls of prokaryotic cells differ in molecular composition and
construction from those of eukaryotes. Most bacterial cell walls contain
peptidoglycan, a network of modified-sugar polymers cross-linked by short
polypeptides. This molecular fabric encloses the entire bacterium and
anchors other molecules that extend from its surface. Archaeal cell walls
contains a variety of polysaccharides and proteins but lack peptidoglycan.
Using a technique called the Gram stain, scientists can classify many
bacterial species into two groups based on differences in cell wall
composition. Gram positive bacteria have simpler walls with a relatively
large amount of peptidoglycan. Gram negative bacteria have less
peptidoglycan and are structurally more complex, with an outer
membrane that contains lipopolysaccharides.

lipopolysaccharide

Peptidoglycan
layer (cell wall)
outer membrane

Plasma
membrane
peptidoglycan layer

Plasma membrane

Gram positive:
Gram negative:

Gram staining is a particularly valuable identification tool in medicine.

Among pathogenic bacteria, gram negative species are generally more
threatening than gram positive species. The lipopolysaccharides on the
walls of gram negative bacteria are often toxic, and the outer membrane
helps protect these bacteria against body’s defenses. Furthermore, gram
negative bacteria are commonly more resistance to antibiotics because
the outer membrane impedes the entry of drugs. Most motile bacteria
propel themselves by flagella, which are structurally and functionally
different from eukaryotic flagella. In heterogeneous environments, many
prokaryotes can move toward or away from certain stimuli. Prokaryotic
cells usually lack complex compartmentalisation. The typical prokaryotic
genome is a ring of DNA that is not surrounded by a mambrane. Some
species also have smaller rings of DNA called plasmids. Prokaryotes
reproduce quickly by binary fission. Many form endospores, which can
remain viable in harsh conditions for centuries. Rapid reproduction and
horizontal gene transfer facilitate the evolution of prokaryotes in
changing environments.

A great diversity of nutritional and metabolic adaptations have evolved in

prokaryotes. Every types of nutrition observed in eukaryotes is
represented among prokaryotes, along with some nutritional modes
unique to prokaryotes.

Major nutritional
modes:

Mode of nutrition Energy source Carbon source Types of

prokaryotes

Photoautotroph Light CO2 Cyanobacteria

Chemoautotroph Inorganic CO2 Sulfolobus

chemicals

Photoheterotrop Light Organic Rhodobacter,

h compounds chloroflexus

Chemoheterotro Organic Organic Clostridium

ph compounds compounds

Prokaryotic metabolism also varies with respects to oxygen. Obligate

aerobes use O2 for cellular respiration and cannot grow without it.
Facultative anaerobes use O2 if it is present but can also grow by
fermentation in an anaerobic environment. Obligate anaerobes are
poisoned by O2. Prokaryotes can also metabolise a wide variety of
nitrogenous compounds. Some can convert atmospheric nitrogen to
ammonia in a process called nitrogen fixation. Besides, metabolic
cooperation also always exist among prokaryotes. Many prokaryotes
depend on the metabolic activities of other prokaryotes. In the
cyanobacterium Anabaena, photosynthetic cells and nitrogen-fixing cells
exchange metabolic products. Some prokaryotes can form surface-coating
colonies called biofilms, which may include different species.

Molecular systematics is illuminating prokaryotic phylogeny.

 Domain Bacteria: Domain Archaea: Domain
Eukarya
:

Proteobacteria Chlamydias Korarchaeotes Eukaryo

Spirochetes Cyanobacteria Gram Euryarchaeotes tes
positive bacteria Crenarchaeotes
Nanoarchaeotes

Universal
ancestor:

A comparison of
the three
Domains:

Characteristics Domain

Bacteria Archaea Eukarya

Nuclear envelope Absent Absent Present

Membrane- Absent Absent Present

enclosed
organelles

Peptidoglycan in Present Absent Absent

cell wall

Membrane lipids Unbranched Some branched Unbranched

hydrocarbons hydrocarbons hydrocarbons
RNA polymerase One kind Several kinds Several kinds

Initiator amino Formylmethionin Methionine Methionine

acid for protein e
synthesis

Introns Rare Present in some Present

genes

Response to the Growth inhibited Growth not Growth not

antibiotics inhibited inhibited
streptomycin
and
chloramphenicol

Histones Absent Present Present

associated with
DNA

Circular Present Present Absent

chromosome

Ability to grow at No Some species No

temperatures >
100oC

Prokaryotes play crucial roles in the biosphere. Decomposition by

heterotrophic prokaryotes and the synthetic activities of autotrophic and
nitrogen-fixing prokaryotes contribute to recycling of elements in
ecosystems. Many prokaryotes live with other organisms in symbiotic
relationships such as mutualism, commemsalism, or parasitism.
Pathogenic prokaryotes typically cause disease by releasing exotoxins or
endotoxins and are potential weapons of bioterrorism. Experiments
involving prokaryotes such as E. coli and A. tumefaciens have led to
important advances in DNA technology. Prokaryotes are major tools in
bioremediation, mining, and the synthesis of vitamins, antibiotics, and
other products.

Protoctista:
Protoctists are an extremely diverse assortment of eukaryotes. Given the
paraphyletic nature of the group once called protista, it isn’t surprising
that few general characteristics of protoctists can be cited without
exceptions. In fact, protoctists exhibits more structural and functional
diversity than other group of organisms. Most protoctists are unicellular,
although there are some colonial and multicellular species. Unicellular
protoctists are justifiably considered the simplest eukaryotes, but at the
cellular level, many protoctists are exceedingly complex – the most
elaborate of all cells. These unicellular organisms must carry out within
the boundaries of a single cell the basic functions performed by all of the
specialised cells in a multicellular organisms. Protoctists are the most
nutritionally diverse of all eukaryotes. Some protoctists are
photoautotrophs, containing chloroplasts. Some are heterotrophs,
absorbing organic molecules or ingesting larger food particles. Still
others, called mixotrophs, combine photoautotrophic and heterotrophic
nutrition. Protoctists habitats are diverse too. Most protoctists are
aquatic, and they are found almost everywhere there is water, including
moist terrestrial habitats such as damp soil and leaf litter. In oceans,
ponds, and lakes, many protoctists are bottom dwellers that attach
themselves to rocks and other substrates or creep through the sand and
silt. In addition to these free-living species, many protoctists live as
symbionts in other organisms.

Endosymbiosis in eukaryotic evolution gave rise to the enermous diversity

of protoctists that exist today. The earliest eukaryotes probably acquired
mitochondria by engulfing alpha proteobacteria. The early origin of
mitochondria is supported by the fact that all eukaryotes studied so far
either have mitochondria or show signs that they had them in the past.
Biologist postulate that later in eukaryotic history, one lineage of
heterotrophic eukaryotes acquired an additional endosymbiont – a
photosynthetic cyanobacterium – that then evolved into plastids. This
plastids-bearing lineage eventually gave rise to red algae and green
algae. These hypotheses are supported by the observation that the DNA of
plastids genes in the red algae and green algae alosely resembles the DNA
of cyanobacteria. In addition, plastids in red algae and green algae are
surrounded by two membranes, which correspond to the inner and outer
membranes of the gram-negative cyanobacteria endosymbionts. On
several occasions during eukaryotic evolution, red algae and green algae
underwent secondary endosymbiosis: they were ingested in the food
vacuole of a heterotrophic eukaryote and became endosymbionts
themselves.

Dinoflagellat
es
 Apicomplexa
ns

2nd endosymbiosis

Cyanobacterium

1st endosymbiosis
Stramenopil
es

Heterotrophic eukaryotes:
2nd endosymbiosis Euglenids

Chlorarachniop
2nd endosymbiosis hytes

The figure below will show a tentative phylogeny of eukaryotes.

Diplomonadida

Parabasala

Euglenozoa

Alveolata

Stramenopila
 Ancestral Cercozoa
eukaryote

Radiolaria

Amoebozoa

Fungi

Choanoflagella
Opisthokonta ta
Animalia

Rhodophyta

Chlorophyta

Plantae
Viridiplantae

Diplomonads have modified mithochondria and two equal-sized nuclei.

Diplopmonads have two equal-sized nuclei and multiple flagella.
Eukaryotic flagella are extensions of the cytoplasm, consisting of bundles
of microtubules covered by the plasma mambrane. They are quite
different from prokaryotic flagella, which are filaments composed of the
globular protein flagellin attacheed to the cell surface. An infamous
example of a diplomonad is Giardia intestinalis, a parasite that inhabits
the intestine of mammals. People most often pick up Giardia by drinking
water contaminated with feces containing the parasites in a dormant cyst
stage. Drinking such contaminated water from a seemingly pristine stream
or river can cause severe diarrhea and ruin a camping trip. Boiling the
water before drinking it kills the cysts.

Parabasalids have modified mitochondria and undulating membrane.

Parabasalids include the trichomonads. The most well-known species is
Trichomonas vaginalis, a common inhabitants of the vagina of human
females. T. vaginalis travels along the mucus-coated lining of the
reproductive and urinary tracts of its host by moving its flagella and by
undulating parts of its plasma membrane. If the normal acidity of the
vagina is disturbed, T. vaginalis can outcompete beneficial microbes and
infect the vagina lining. Such infections, which cab be sexually
transmitted, can also occur in the urethra of males, though often without
symptoms. Genetic studies of T. vaginalis suggest that the species became
pathogenic when some of these parabasalids acquired a particular gene
through horizontal gene transfer from bacteria that also dwell in the
vagina. The gene allows T. vaginalis to feed on epithelial cells, resulting in
infection.

Euglenozoans have flagella with spiral or crystalline rod inside it. The
euglenozoans is a diverse clade that includes predatory heterotrophs,
photosynthetic autotrophs, and pathogenic parasites. The main feature
that distinguishes them in this clade is the presence of spiral or crystalline
rod of unknown function inside their flagella. Most euglenozoans also have
disk-shaped mitochondrial cristae. The two best studied groups of
euglenozoans are the kinetoplastids and the euglenids. Kinetoplastids
have a single, large mitochondrion that contains an organised mass of
DNA called kinetoplast. Kinetoplastids include free-living consumers of
prokaryotes in freshwater, marine, and moist terrestrial ecosystems, as
well as species that parasites animals, plants, and other protoctists. For
example, kinetoplastids in the genus Trypanosoma cause sleeping
sickness in humans, a disease spread by the African tsetse fly that is
invariably fatal if left untreated. Trypanosoma also cause Chagas’ disease,
which is transmitted by bloodsucking insects and can lead to congestive
heart failure. Euglenids have a pocket at one end of the cell from which
one or two flagella emerge. Paramylon, a glucose polymer that function as
storage molecule, is also characteristic of euglenids. Many species of the
euglenid Euglena are autotrophic, but when sunlight is unavailable, they
can become heterotrophic, absorbing organic nutrients from their
environment. Many other euglenids can engulf prey by phagocytosis.

Alveolates have membrane-bounded sacs (alveoli) beneath the plasma

membrane. The function of the alveoli is unknown; researchers
hypothesise that they may help stabilise the cell surface or regulate the
cell’s water and ion content. Alveolata includes three groups:
dinoflagellates, apicomplexans, and ciliates. Dinoflagellates are abundant
components of both marine and freshwater phytoplankton. There are also
heterotrophic dinoflagellates. Of the several thousand known
dinoflagellate species, most are unicellular, but some are colonial. Each
has a characteristic shape that in many species is reinforced by internal
plates of cellulose. Two flagella located in perpendicular grooves in this
dinoflagellates spin as they move through the water. Dinoflagellate
blooms-episodes of explosive population growth- can cause a phenomenon
called the ‘red tide’ in coastal waters. The blooms appear brownish red or
pinkish orange because the presence of carotenoids, the most common
pigments in dinoflagellate plastids. Toxins produced by certain
dinoflagellates can cause massive kills of invertebrates and fishes.
Humans who consume molluscs that have accumulated the toxins are
affected as well, sometimes fatally. Some dinoflagellates are spectaculary
bioluminescent: an ATP-driven chemical reaction creates an eerie glow at
night when waves, boats, or swimmers agigate seawater with dense
population of dinoflagellates. One possible function of this
bioluminescence is that when the water is disturbed by organisms that
feed on dinoflagellates, the light attracts fishes that eat those predators.
Some dinoflagellates are mutualistic symbionts of coral polyps, animals
that build coral reefs. The dinoflagellates’ photosynthetic output is the
main food for reef communities. All apicomplexans are parasites of
animals, and some cause serious human disease. The parasites spread
through their host as tiny infectious cells called sporozoites.
Apicomplexans are so named because one end of the sporozoites cell
contains a complex of organelles specialised for penetrating host cells and
tissues. Apicomplexans also have a nonphotosynthetic plastid, called the
apicoplast. Although apicomplexans are nonphotosynthetic, their
apicoplast has vital functions, such as the synthesis of fatty acids. Most
apicomplexans have intricate life cycles with both sexual and asexual
stages. Those life cycles often require two or more different host species
for completion. For example, plasmodium, the parasite that cause malaria,
lives in both mosquitoes and humans. An infected Anopheles mosquito
bites a person, injecting Plasmodium sporozoites in its saliva. The
sporozoites enter the person’s liver cells. After several days, the
sporozoites undergo multiple divisions and become merozoites, which use
their apical complex to penetrate red blood cells. The merozoites divide
asexually inside the red blood cells. At intervals of 48 or 72 hours, large
numbers of merozoites break out of the blood cells, causing periodic chills
and fever. Some of the merozoites infect new red blood cells and some
merozoites form gametocytes. Another Anopheles mosquito bite the
infected preson and picks up Plasmodium gametocytes along with blood.
Gamets form from gametocytes. Fertilisation occurs in the mosquito’s
digestive tract, and a zygote forms. The zygote is the only diploid stage in
the life cycle. An oocyst develops from the zygote in the wall of the
mosquito’s gut. The oocyst releases thousands of sporozoites, which
migrate to the mosquito’s salivary gland. Ciliates are large, varied group
of protoctists named for their use of cilia to move and feed. The cilia may
be clustered in a few rows or tufts. In certain species, rows of tightly
packed cilia function collectively in locomotion. Other ciliates scurry about
on leglike structures constructed from many cilia bonded together. A
submembrane system of nicrotubules coordinates ciliary movements. A
distinctive feature of ciliates is the presence of two types of nuclei: large
macronuclei and tiny micronuclei. A cell may have one or more nucleus of
each type. Each macronucleus typically contains dozens of copies of the
ciliate’s genome. The genes are not organised in chromosomes but
instead are packaged in smaller units, each bearing many duplicates of
just a few genes. Macronuclear genes control the everyday functions of
the cell, such as feeding, waste removal, and maintaining water balance.
Ciliates generally reproduce asexually by binary fission, during which the
macronucleus elongates and splits, rather than undergoing mitotic
division. Genetic variation results from conjugation, a sexual procss in
which two individuals exchange haploid micronuclei.

Stramenopiles have hairy and smooth flagella. The clade stramenopila

includes several groups of heterotrophs as well as certain groups of algae.
Stramenopiles can be divided into Oomycetes, Diatoms, Golden algae, and
Brown algae. Oomycetes have hyphae that absorb nutrients. Oomycetes
include water molds, white rusts, and downy mildew. Early studies
suggested that these organisms were fungi. For example, many
oomycetes have multinucleated filaments(hyphae) that resemble fungal
filaments. However, there are many differences between oomycetes and
fungi. Oomycetes typically have cell walls made of cellulose, whereas the
cell walls of fungi consist mainly of chitin. The diploid condition, which is
reduced in fungi, predominates in most oomycetes life cycle. Oomycetes
also have flagellates cells, whereas almost all fungi lack flagella.
Molecular systematics has confirmed that oomycetes are not closely
related to fungi. Their superficial similarity is a case of convergent
evolution. In both oomycetes and fungi, the high surface-to-volume ratio
of filamentous structures enhances the uptake of nutrients from the
environments. Although oomycetes descended from plastid-bearing
ancestors, they no longer have plastids and no longer carry out
photosynthesis. Instead, they acquire nutrients mainly as decomposers or
parasites. Most watermolds are decomposers that grow as cottony masses
on dead algae and animals, mainly in fresh water. White rusts and downy
mildews generally live on land as parasites of plants. They are dispersed
primarily by wind blown spores, although they also form flagellated
zoospores at some point during their life cycles. Diatoms(bacillariophytes)
are unicellular algae that have a unique glass-like wall made of hydrated
silica embedded in an organic matrix. These walls provide effective
protection from the crushing jaws of predators. Much of the strength of
diatoms comes from the delicate lacework of holes and grooves in their
walls- if the walls were smooth, it would take 60% less force to crush
them. Most of the year, diatoms reproduce asexually by mitosis, with each
daughter cell receiving half of the parental cell wall and generating a new
half that fits inside it. Some species form cysts as resistant stage. Sexual
reproduction is not common in diatoms. When it occurs, it involves the
formation of eggs and sperms; sperm cells may be amoeboid or
flagellated, depending on species. Diatoms are major component of
phytoplankton both in ocean and in lakes. Like golden algae and brown
algae, diatoms store their food reserves in the form of a glucose polymer
called laminarin. Some diatoms store food as oil. Golden algae, or
chrysophytes, are named for their colour, which results from their yellow
and brown carotenoids. The cells of golden algae are typically
biflagellated, with both flagella attached near one end of the cell. Many
golden algae are components of freshwater and marine plankton. While all
golden algae are photosynthetic, some species are mixotrophic, and can
also absorb dissolved organic compounds or ingest food particles and
prokaryotes by phagocytosis. Most species are unicellular, but some are
colonial. If cell density exceeds a certain level, many species form
resistant cysts that can survive for decades. Brown algae or phaeophytes
are the largest and most complex algae. All are multicellular, and most are
marine. Brown algae are especially common along temperate coasts,
where the water is cool. They owe their characteristic brown or olive
colour to the carotenoids in their plastids, which are homologous to the
plastids of gloden algae and diatoms. Brown algae include many of the
species commonly called seaweeds. Seaweeds have the most complex
multicellular anatomy of all algae. Some even have specialised tissues and
organs that resemble those in plants. But various evidences indicates that
the similarities evolved independently in the algal and plants lineage and
are thus analogous, not homologous. A variety of life cycles have evolved
among the multicellular algae. The most complex life cycles include an
alternation of generations, the alternation of multicellular haploid and
diploid forms. Although haploid and diploid conditions alternate in all
sexual life cycles, the term alternation of generations applies only to life
cycles in which both haploid and diploid stages are multicellular. The
complex life cycle of the brown algae Laminaria is an example of
alternation of generations. The sporophytes(2n) of this seaweed are
usually found in water just below the line of the lowest tides, attached to
rocks by branching holdfasts. In early spring, at the ends of the main
growing season, cells on the surface of the blade develop into sporangia,
which produce zoospores by meiosis. About half of the zoospores develop
into male gametophytes and half into female female gametophytes. Male
gametophytes release sperms, and female gametophytes produce eggs,
which remain attached to the female gametophyte. Eggs secrete a
chemical signal that attracts sperms of the same species, thereby
increasing the probability of fertilisation in ocean. After the sperm fertilise
the eggs, the zygotes grow into new sporophytes, starting life attached to
the remains of the female gametophyte.

Cercozoans and radiolarians have threadlike pseudopodia. Cercozoa

contains a diversity of species that are among the organisms referred to
as amoebas. Amoebas were formerly defined as protoctists that move and
feed by means of pseudopodia, extensions that may bulge from virtually
anywhere on the cell surface. When an amoeba moves, it extends a
pseudopodium and anchors the tip, and then more cytoplasm streams into
the pseudopodium. However, based on the molecular systematics, it is
now clear that amoebas do not constitute a monophyletic group but are
dispersed across many distantly related eukaryotic taxa. Those that
belong to the clade cercozoa are distinguished morphologically from most
other amoebas by their threadlike pseudopodia. Cercozoans include
chlorarachniophytes and foraminiferans. Protoctists in another clade,
radiolaria, also have threadlike pseudopodia and are closely related to
cercozoans. Foraminiferans, or forams, are named for their porous shells,
called tests. Foram tests are generally multichambered and consist of
organic material hardened with calcium carbonate. The pseudopodia that
extend through the pores function in swimming, test formation, and
feeding. Many forams also derive nourishment from the photosynthesis of
symbiotic algae that live within the tests. Forams are found in both the
ocean and freshwater. Most species live in the sand or attached
themselves to rocks or algae, but some are abundant in plankton. The
largest forams, though single-celled, grow to a diameter of several
centimeters. 90% of all identified species of forams are known from
fossils. Along with the calcerous remains of other protoctists, the
fossilised tests of forams are components of marine sediments, including
sedimentary rocks that are now land formations. Forams fossils are
excellent markers for correlating the ages of sedimentary rocks in
different parts of the world. Radiolarians are mostly marine protoctists
whose tests are fused into one delicate piece, which is generally made of
silica. The pseudopodia of radiolarians, known as axopodia, radiate from
the central body and are reinforced by bundles of microtubules. The
microtubules are covered by thin layer of cytoplasm, which surrounds
through phagocytosis smaller microorganisms that become attached to
the axopodia. Cytoplasmic streaming then carries the engulfed prey into
the main part of the cell. After radiolarians die, their tests settle to the
seafloor, where they have accumulated as an ooze that is hundreds of
meters thick in some locations.
Amoebozoans have lobe-shaped pseudopodia. Amoebozoans include
gymnamoebas, entamoebas, and slime molds. Gymnamoebas constitute a
large and varied group of amoebozoans. These unicellular protoctists are
ubiquitous in soils as well as freshwater and marine environments. Most
are heterotrophs that actively seek and consume bacteria and other
protoctists. Some gymnamoebas also feed on detritus. Entamoebas are
parasites that infect all classes of vertebrates as well as some
invertebrates. Slime molds, or mycetezoans, were once thought to be
fungi because, like fungi, they produce fruiting bodies that aid in spore
dispersal. However, the resemblance between slime molds and fungi
appears to be another example of evolutionary convergence. Molecular
systematics places slime molds in the clade amoebozoa and suggests that
they descended from unicellular, gymnamoebas-like ancestors.

Red algae, or rhodophytes have an accessory pigment called

phycoerythrin and without flagellated stages. Red algae are the most
abundant large algae in the warm coastal waters of tropical oceans. Their
accessory pigments allow them to absorb blue and green light, which
penetrate relatively far into the water. There are also freshwater and
terrestrial species. Most red algae are multicellular, and the largest are
included in the informal designation “seaweeds”. The thalli of many red
algae are filamentious, often branched and interwoven in lacy patterns.
The base of the thallus is usually differentiated as a simple holdfast. Red
algae have especially diverse life cycles, and alternation of generations is
common. But unlike other algae, they have no flagellated stages in their
life cycle and depends on water currents to bring gamates together for
fertilisation.

Green algae, or chlorophytes are named for their grass-green

chloroplasts. In their ultrastructure and pigment composition, these
chloroplasts are much like those of organisms we traditionally call plants.
Molecular systematics and cellular morphology leave little doubt that
green algae and land plants are closely related. In fact, some systematics
now advocate the inclusion of green algae in an expanded plant kingdom,
viridiplantae.

Plants:
Land plants evolved from green algae. Researchers have identified green
algae called charophyceans as the closest relatives of land plants.

Charophyceans Bryophytes Seedless

vascular plants Gymnosperms Angiosperms
Many key characteristics of land plants also appears in a variety of
protoctists, primarily algae. For example, plants are multicellular,
eukaryotics, photosynthetic autotrophs, as are brown, red, and certain
green algae. Plants have cell walls made of cellulose, and so do green
algae, dinoflagellates, and brown algae. And chloroplasts with chlorophyll
a and b are present in green algae, euglenids, and a few dinoflagellates,
as well as in plants. There are four key traits, however, that lands plants
share only with the charophyceans, strongly suggesting a close
relationship between the two groups:

1. Rose-shaped complexes for cellulose synthesis. The cells of both

land plants and charophyceans have rosette cellulose-synthesising
complexes. These are rose-shaped arrays of proteins in the plasma
membrane that synthesise the cellulose microfibrils of the cell walls.
In contrast, linear arrays of proteins synthesise cellulose in
noncharophycean algae. These differences indicate that the
cellulose walls in plants and charophyceans evolved independently
of those in other algae.

2. Peroxisome enzymes. The peroxisome of both land plants and

charophyceans contain enzymes that help minimise the loss of
organic products as a result of photorespiration. The peroxisome of
other algae lack these enzymes.

3. Structure of flagellated sperm. In species of land plants that have

flagellated sperm, the structure of the sperm closely resembles that
of charophyceans sperm.

4. Formation of a phragmoplast. Certain details of cell division occur

only in land plants and certain charophyceans, including the genera
Chara and Coleochaete. For example, the synthesis of new cross-
walls during cell division involves the formation of a phragmoplast,
an alignment of cytoskeletal elements and golgi-derived vesicles
across the midline of the dividing cell.

Over the past decade, researchers involved in an international initiative

called “Deep Green” have conducted a large-scale study of major
transitions in plants evolution, analysing genes from a wide range of
plants and algal species. Comparisons of both nuclear and chloroplast
genes agree with the morphological and biochemical data in pointing to
charophyceans as the closest relatives of land plants. Note that this does
not mean that these living algae are the ancestors of plants; however,
they do offer a glimpse of what those ancestors might have been like.
Many species of charophyceans algae inhabits shallow waters around the
edges of ponds and lakes, where they are subject to occasional drying. In
such environments, natural selection favours individual algae that can
survive periods when they are not submerged in water. In charophyceans,
a layer of a durable polymer called sporopollenin prevents exposed
zygotes from drying out. An ancestral form of this chemical adaptation
may have also been the precursor to the tough sporopollenin walls that
encase plant spores. It is likely that the accumulation of such traits by at
least one population of charophyceans ancestors enabled their
descendants- the first land plants – to live permently above the waterline.
These evolutionary novelties opened an expanse of terrestrial habitat, a
new frontier that offered a enormous benefits. The bright sunlight was
unfiltered by water and planktons; the atmosphere had an abundance of
CO2; the soil was rich in mineral nutrients; and initially there were
relatively few herbivores and pathogens. Benefiting from these
environmental opportunities became possible as adaptations evolved in
plants that allowed them to survive and reproduce on land.

Land plants possess a set of derived terrestrial adaptations. Many of the

adaptations that emerged after land plants diverged from their
charophyceans relatives facilitated survival and reproduction on dry land.
Where exactly is the line dividing land plants from algae? Systematists are
currently debating the boundaries of the plant kingdom. The traditional
scheme equates the kingdom plantae with embryophytes. Some plant
biologists now propose that the boundaries of the plants kingdom should
be expanded to include the green algae most closely related to plants-the
charophyceans and a few related group-and named kingdom streptophyta.
Others suggest an even broader definition of plants that also includes
chlorophytes in a kingdom viridiplantae. Since the debate is still ongoing,
this text retains the embryophytes definition of the plant kingdom and
uses kingdom plantae as the formal name for the taxon. Five key traits
appear in nearly all land plants but are absents in the charophyceans:
apical meristems; alternation of generations; walled spores produced in
sporangia; multicellular gametangia; and multicellular, dependent
embryos.

1. Apical meristems: In terrestrial habitats, a photosynthetic organism

finds essential resources in two very different places. Light and CO2
 are mainly available above-ground; water and mineral nutrients are
found mainly in the soil. Though plants cannot move from place to
place, their roots and shoots can elongate, increasing exposure to
environmental resources. This growth in length is sustained
throughout the plant’s life by the activity of apical meristems,
localised regions of cell division at the tips of shoots and roots. Cells
produced by apical meristems differentiate into various tissues,
including a surface epidermis that protects the body and several
types of internal tissues. Shoot apical meristems also generates
leaves in most plants. Thus, the complex bodies of plants show
structural specialisation for subterranean and aerial organs- roots
and leaf-bearing shoots, respectively, in most plants.

2. Alternation of generations: The life cycles of all land plants alternate

between two different multicellular bodies, with each form
producing the other. This type of reproductive cycle, called
alternation of generations, also evolved in various groups of algae
but does not occur in the charophyceans, the algae most closely
related to land plants. We can infer that alternation of generations is
derived characteristic of land plants as it was not present in the
ancestor common to land plants and charophyceans.

3. Walled spores produced in sporangia: Plant spores are haploid

reproductive cells that have the potential to grow into multicellular,
haploid gametophytes by mitosis. The polymer sporopollenin makes
the walls of plant spores very tough and resistant to harsh
environments. This chemical adaptation makes it possible for spores
to be dispersed through dry air without harm. The sporophyte has
multicellular organs called sporangia that produce plant spores.
Within a sporangium, diploid cells called sporocytes, also known as
spore mother cells, undergo meiosis and generate the hapoid
spores. The outer tissues of the sporangium protect the developing
spores until they are released into the air.

4. Multicellular gametangia: Another feature distinguishing early land

plants from their algal ancestors was the production of gametes
within multicellular organs called gametangia. The female
gametangia are called archegonia while the male gametangia are
called antheridia.

5. Multicellular, dependent embryos: Multicellular plant embryos

develop from zygotes that are retained within tissues of the female
parent. The parental tissues provide the developing embryo with
nutrients, such as sugars and amino acids. The embryo has
specialised placental transfer cells, sometimes present in the
 adjacent maternal tissue as well, which enhance the transfer of
nutrients from parent to embryo through elaborate ingrowth of the
wall surface. The multicellular, dependent embryo of land plants is
such a significant derived trait that land plants are also known as
embryophytes.

Red algae:

Ancestral alga: Chlorophyt

es:

Charophyce
ans:

Viridiplantae

Streptophyta

Embryophy
Plantae
tes:

Ten phyla of extant plants:

Common name Approxiamte number of

extant species

Bryophytes
(nonvascular
plants)
Hepatophytes Liverworts 9000

Anthocerophytes Hornworts 100

Bryophytes mosses 15000

Vascular plants
Seedless vascular
plants
Lycophytes Club mosses, spike 1200
mosses, and quillworts

Pterophytes Ferns, horsetails, and 12000

whisk ferns

Seed plants
Gymnosperms

Ginkophytes Ginko 1

Cycadophytes Cycads 130

Gnetophytes Gnetum, ephedra, and 75

welwitschia

Coniferophytes conifers 600

Angiosperms

Anthophytes Flowering plants 250000

Bryophytes are represented today by three phyla of small herbaceous

plants: liverworts, hornworts, and mosses. Liverworts and hornworts are
named for their shapes, plus the suffix wort. Mosses are most familiar
bryophytes, although some plants commonly called mosses are not
mosses at all. These include Irish moss, reindeer moss, club mosses, and
Spanish mosses. Note that the term Bryophyta and bryophytes are not
synonymous. Bryophyta is the taxonomic name for the phylum that
consists solely of mosses. The term bryophytes is used informally to refer
to all nonvascular plants. Bryophytes acquired many unique adaptations
after their evolutionary split from the ancestors they share with living
vascular plants. Nevertheless, living bryophytes likely reflect some traits
of the earliest plants. The oldest known fossils of plant fragments, for
example, include tissues that look very much like the interior of
liverworts. Unlike vascular plants, in all three bryophyte phyla the
gametophytes are larger and longer-living than sporophytes. Sporophytes
are typically present only part of the time. If bryophyte spores are
dispersed to a favourable habitat, such as moist soil or tree bark, they
may germinate and grow into gametophytes. Germinating moss spores,
for example, characteristically produce a mass of green, branched, one-
cell-thick filaments known as protonema(plural: protonemata). A
protonema has a large surface area that enhances absorption of water and
minerals. In favourable conditions, a protonema produces one or more
buds, each with an apical meristem that generates a gamet-producing
structure known as gametophore. Together, a protonema and
gametophore make up the body of the moss gametophyte. Although
bryophyte sporophytes are usually green and photosynthetic when young,
they cannot live independently. They remain attached to their parental
gametophytesm from which they absorb sugars, amino acids, minerals,
and water. Bryophytes have the samllest and simplest sporophytes of all
extant plant groups, consistent with the hypothesis that larger and more
complex sporophytes evolved only after in vascular plants. A typical
sporophyte consists of a foot, a seta, and a sporangium. Embedded in the
archegonium, the foot absorbs nutrients from the gametophyte. The seta,
or stalk, conducts these materials to the sporangium, also called a
capsule, which uses them to produce spores by meiosis. One capsule can
generate up to 50 million spores. In most mosses, the seta becomes
elongated, enhancing spore dispersal by elevating the capsule. An
immaturre sapsule has a protective cap of gametophyte tissue called
calyptra, which is shed when the capsule is mature. In most moss species,
the upper part of the capsule features a ring of tooth-like structures
known as the peristome. The peristome is specialised for gradual spore
discharge, taking advantage of periodic wind gusts that can carry spores
long distances. Hornworts and moss sporophytes are larger and more
complex than those of liverworts. Both hornworts and moss sporophytes
also have specialised pores called stomata, which are also found in all
vascular plants. These stomata support photosynthesis by allowing the
gaseous exchanges between the outside air and the sporophyte interior.
Stomata are the main avenues by which water evaporates from the
sporophyte. In hot, dry comditions, the stomata can close, minimising
water loss. The fact that stomata are present in mosses and hornworts but
absent in liverworts suggests three possible hypotheses for their
evolution. If liverworts are the deepest-branching lineage of land plants,
then stomata evolved once in the ancestor of hornworts, mosses, and
vascular plants, if hornworts are the deepest-branching lineage, then
stomata may have evolved once and then been lost in the liverwort
lineage. Or perhaps hornworts acquired stomata independently of mosses
and vascular plants. Wind dispersal of lightweight spores has distributed
mosses around the world. These plants are particularly common and
diverse in moist ferests and wetlands, where they form habitats for tiny
animals. Some moss species even inhabits such extreme environments as
mountaintops, tundra, and deserts. Many mosses exist in very cold or dry
habitats because they can survive the loss of most of their body water,
then rehydrate when moisture is available. Few vascular plants can
survive the same degree of desiccation. Moreover, phenolic compounds in
moss cell walls absorb damaging levels of radiation present in deserts or
at high altitudes and latitudes. One wetland moss genus, Sphagnum, or
peat moss, is especially widespred, forming extensive deposits of partially
decayed organic material known as peat. Boggy regions dominated by this
moss are called peat bogs. Because of the resistant phenolic compounds
embedded in its cell walls, sphagnum does not decay readily. In addition,
it secretes compounds that may reduce bacterial activity. Low
temperature and nutrient level in peat bogs also inhibit decay. As a result,
peat bogs can preserve mummified corpses for thousands of years.
Worldwide, an estimated 400 billion tons of organic carbon are stored in
peat. These carbon reservoirs help stabilise global atmospheric CO2
concentrations.

Ferns and other seedless vascular plants formed the first forests. Whereas
bryophytes or bryophyte-like plants were the prevelent vegetation during
the first 100 million years of plants evolution, vascular plants dominate
most landscapes today. Living seedless vascular plants provide insights
into plant evolution during the Carboniferous period, when vascular plants
began to diversify but most groups of seed plants had not yet evolved.
The sperms of ferns and all other seedless vascular plants are flagallated
and must swim through a film of water to reach eggs, as in bryophytes.
Due to these swimming sperms, as well as their fragile gametophytes,
living seedless vascular plants are most common in damp environments.
Thus it is likely that before the emergence of seed plants, most plant life
on earth was limited to relatively damp habitats. Fossils of the
forerunners of today’s vascular plants date back about 420 million years.
Unlike bryophytes, these species had branched sporophytes that were not
dependent on gametophytes for growth. Although these plants grew no
taller than about 50 cm, their branching made possible more complex
bodies with multiple sporangia. This evolutionary development facilitated
greater production of spores and increased survival despite herbivory, for
even if some sporangia were eaten, others might survive. The ancestors of
vascular plants already displayed some derived traits of living vascular
plants, but they lacked other key adaptations that evolved later. This
section describes the main traits that characterise living vascular plants:
life cycles with dominant sporophytes, transport in vascular tissues, and
the presence of roots and leaves, including spore-bearing leaves called
sporophylls.

1. Life cycles with dominant sporophytes: In contrast with bryophytes,

sporophytes of seedless vascular plants are the larger generation,
 as in the example of the familiar leafy fern plant. The gametophytes
are tiny plants that grow on or below the surface.

2. Transport in xylem and phloem: Vascular plants have two vascular

tissue: xylem and phloem. Xylem conducts most of the water and
minerals. Xylem of all vascular plants includes dead cells called
tracheids. The lignin in xylem enables most vascular plants to grow
taller than bryophytes. Phloem, a living tissue, conducts sugars and
other organic nutrients.

3. Evolution of roots: Unlike the rhizoids of bryophytes, roots play an

important role in absorbing water and nutrients. Roots may have
wvolved from subterranean stems. It is unclear whether rots evolved
independently in different lineages.

4. Evolution of leaves: In terms of evolution, leaves are categorised

into two types: microphylls and megaphylls. Microphylls, leaves with
a single vein, evolved first and are typical of lycophytes. Almost all
other vascular plants have megaphylls, leaves with a highly
branched vscular system. Megaphylls are usually larger, with more
photosynthetic productivity.

5. Sporophylls and spore variations: Sporophylls are modified leaves

with sporangia. Most seedless vascular plant species are
homosporous, producing one type of spore, which usually develops
into a bisexual gametophyte. All seed plants and some seedless
vascular plant species are heterosporous, having two types of
spores that give rise to male and female gametophytes.

Fossils and comparative studies of living plants offer clues about the
origin of seed plants some 360 million years ago. Seeds changed the
course of plant evolution, enabling their bearers to become the dominant
producers in most of the terrestrial ecosystems and to make up the vast
majority of plant biodiversity.

The reduced gametophytes of seed plants are protected in ovules and

pollen grains. There are several key terrestrial characteristics that seed
plants added to those already present in bryophytes and seedless
vascular plants. In addition to seeds, the following are common to all seed
plants: reduced gametophytes, heterospory, ovules, and pollen.

1. Advantages of reduced gametophytes: Mosses and other bryophytes

have life cycles dominated by gametophytes, whereas ferns and
other seedless vascular plants have sporophyte-dominated life
cycles. The evolutionary trend of gametophyte reduction continued
further in the vascular plant lineage that led to seed plants. While
 the gametophytes of sedless vascular plants are visible to the naked
eye, the gametophytes of seed plants are mostly microscopic. This
miniaturation allowed for an important evolutionarty innovation in
seed plants: their tiny gametophytes can develop from spores
retained within the sporangia of the parental sporophytes. This
arrangement protects the delicate female gametophytes from
environmental stresses. The moist reproductive tissues of the
sporophyte shield the gametophytes from drought conditions and
from UV radiation. This relationship also enables the dependent
gametophytes to obtain nutrients from the sporophytes. In contrast,
the free-living gametophytes of seedless plants must fend for
themselves.

2. Heterospory: The closest relatives of seed plants are all

homosporous, suggesting that seed plants also had homosporous
ancestors. At some point, seed plants or their ancestors became
heterosporous: megasporangia in megasporophylls produce
megaspores that give rise to female gametophytes, and
microsporangia in microsporophylls produce microspores that give
rise to male gametophytes. Each megasporangium has a single
functional megaspore, whereas each microsporangium contains vast
numbers of microspores.

3. Ovules and production of eggs: Although a few species of seedless

vascular plants are heterosporous, seed plants are unique in
retaining the megaspore within the parent sporophyte. Layers of
sporophyte tissue called integuments envelop and protect the
megasporanguim. Gymnosperm megaspores are surrounded by one
integuments, whereas those in angiosperms usually have two
integuments. The whole structure-megasporangium, megaspores,
and their integument- is called an ovule. Inside each ovule, a female
gametophyte develops from a megaspore and produces one or more
egga cells.

4. Pollen and production of sprem: microspores develop into pollen

grains, which contain the male gametophytes of seed plants.
Protected by a tough coat containing the polymer sporopollenin,
pollen grains can be carried away from their parent plant by wind or
by hitchhiking on the body of an animals that visits the plant to
feed. The transfer of pollen to the part of a seed plant containing the
ovules is called pollination. If a pollen grain germinates, it gives rise
to a pollen tube that discharges two sperms into the female
gametophytes within the ovule.
We have been discussing characteristics of seed plants, but what exactly
is a seed? If a sperm fertilises an egg of a seed plants, the zygote grows
into a sporophyte embryo. The whole ovule develops into a seed, which
consists of the embryo, along with food supply, packaged within a
protective coat derived from the integument. The evolution of seeds
enabled plants bearing them to better resist harsh environments and to
disperse offspring more widely. Until the advent of seeds, the spore was
the only protective stage in any plant life cycle. For example, moss spores
may survive even if the local environment becomes too cold, too hot, or
too dry for the mosses themselves to live. Their tiny size enables the moss
spores to be dispersed in a dormant state to a new area, where they can
germinate and give rise to new moss gametophytes if and when the
environment is favourable enough for them to break dormancy. Spores
were the main way that mosses and other seedless plants spread over
Earth for first 100 million years of plant life on land. In contrast to a spore,
which is single-celled, a seed is a multicellular structure that is much more
resistant and complex. Its protective coat is derived from the integument
of the ovule. After being released from the parent plant, a seed may
remain dormant for days, months, and even years. Under favourable
conditions, it can then germinate, with the sporophyte embryo emerging
as a seedling. Some seeds drop close to their parent sporophyte plant;
others are carried far by the wind or animals.

Gymnosperms bear naked seeds, typically on cones. Among the

gymnosperms are cone-bearing plants called conifers, which include such
trees as pines, firs and red-woods. Fossil evidence reveals that the late
Devonian period, some plants had begun to acquire adaptations that
characterise seed plants. The first seed-bearing plants to appear in the
fossil record were gymnosperms dating from around 360 million years
ago, more than 200 million years before the first angiosperm fossils.
These early gymnosperm species became extinct, along with several later
gymnosperm lineages. Although the relationships between extinct and
surviving lineage of seed plants remain uncertain, morphological and
molecular evidence places surviving lineages of seed plants into two
clades: the gymnosperms and the angiosperms. Early gymnosperms lived
in Carboniferous ecosystems still dominated by lycophytes, horsetails,
ferns, anf other seedless vascular plants. As the Carboniferous period
gave way to the Permain, markedly drier climatic conditions favoured the
spread of gymnosperms. The flora and fauna changed dramatically, as
many groups of organisms disappeared and others became prominent.
Though most pronounced in the seas, the changeover also affected
terrestrial life. For example, the lycophytes, horsetails, and ferns that
dominated the Carboniferous period were largely replaced by
gymnosperms, which were more suited to the drier climate. In such
gymnosperms as pines and firs, among the adaptation to arid conditions
are their needle-shaped leaves, which have thick cuticle and relatively
small surface areas. The largest gymnosperm phylum is the Phylum
Coniferophyta, consisting of about 600 species of conifers. Many are large
trees, such as cypresses and redwoods. A few conifer species dominate
vast forested regions of the northern hemisphere, where the growing
season is relatively short because of latitude or altitude. Most conifers are
evergreens; they retain their leaves throughout the year. Even during the
winter, a limited amount of photosynthesis occurs on sunny days. When
spring comes, conifers already have fully developed leaves that can take
advantage of the sunier, warmer days. Some conifers, such as the dawn
redwood, tamarack, and larch, are deciduous trees that lose leaves each
autumn.