Biodiversity Repaired)

Biodiversity: The Geologic Record: Relative duration of Eons and Eras: Archaean

Period

Epoch

Age (millions of years ago) Approx.4 600

Important events

3800

Oldest known rock on earth’s surface. Oldest fossils of cells(prokaryotes). Concentration of atmospheric O2 begins to increase. Oldest fossils of eukaryotic cells. Diverse algae and soft-bodied invertebrate animals.

3500 2700 Proteroz oic

2200 600

Phaneroz oic: Paleozoic

Mesozoic

Origin of Earth.

Cambrian

488-5542

Sudden increase in diversity of many animal phyla (Cambrian explosion). Marine algae abundant; colonisaton of land by plants and arthropods. Diversificaton of early vascular plants. Diversification of bony fishes; first tetrapods and insects.

Ordovicia n

443.7488

Silurian

416-443

Devonian

359.2416

Carbonife rous

299-359

Extensive forests of vascular 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.

Triassic

199.6299

Cone-bearing plants dominate landscape; radiation of dinasaurs; origin of mammallike reptiles.

Cenozoic

Jurassic

145.5199

Gymnosperms continue as dominant plants; dinasaurs abundant and diverse.

Cretaceou s

65.5-145

Flowering plants appear; many groups of organisms become extinct at the end of period(Cretaceous extniction).

Paleoce ne Eocene

55.8-65

Major radiation of mammals, birds, and pollinating insects. Angiosperm dominance increase; continued radiation of most modern mammalian orders.

Oligoce ne

23-33.9

Origin of many primate groups, including apes.

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 ene Holocen e

0.01-1.8

Ice ages; humans appear.

Now-0.01

Historacal time.

Paleogene

Neogene

33.955.8

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

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

Domain

typically have diameters in the range of 1-5 µm, much smaller than the 10100 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 chemicals

CO2

Sulfolobus

Photoheterotrop h

Light

Organic compounds

Rhodobacter, chloroflexus

Chemoheterotro ph

Organic compounds

Organic compounds

Clostridium

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:

Proteobacteria Chlamydias Spirochetes Cyanobacteria Gram positive bacteria

Domain Archaea:

Korarchaeotes Euryarchaeotes Crenarchaeotes Nanoarchaeotes

Domain Eukarya :

Eukaryo tes

Universal ancestor:

A comparison of the three Domains: Characteristics

Domain Bacteria

Archaea

Eukarya

Nuclear envelope

Absent

Absent

Present

Membraneenclosed organelles

Absent

Absent

Present

Peptidoglycan in cell wall

Present

Absent

Absent

Membrane lipids

Unbranched hydrocarbons

Some branched hydrocarbons

Unbranched hydrocarbons

RNA polymerase

One kind

Several kinds

Several kinds

Initiator amino acid for protein synthesis

Formylmethionin e

Methionine

Methionine

Introns

Rare

Present in some genes

Present

Response to the antibiotics streptomycin and chloramphenicol

Growth inhibited

Growth not inhibited

Growth not inhibited

Histones associated with DNA

Absent

Present

Present

Circular chromosome

Present

Present

Absent

Ability to grow at temperatures > 100oC

No

Some species

No

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

Heterotrophic eukaryotes: 2nd endosymbiosis

2nd endosymbiosis

Stramenopil es

Euglenids

Chlorarachniop hytes

The figure below will show a tentative phylogeny of eukaryotes. Diplomonadida Parabasala Euglenozoa

Alveolata

Stramenopila

Ancestral eukaryote

Cercozoa

Radiolaria Amoebozoa

Fungi

Opisthokonta

Choanoflagella 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. vascular plants

Charophyceans Gymnosperms Angiosperms

Bryophytes

Seedless

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 crosswalls 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 tes:

Plantae

Ten phyla of extant plants: Common name

Approxiamte number of extant species

Hepatophytes

Liverworts

9000

Anthocerophytes

Hornworts

100

Bryophytes (nonvascular plants)

Bryophytes

mosses

15000

Lycophytes

Club mosses, spike mosses, and quillworts

1200

Pterophytes

Ferns, horsetails, and whisk ferns

12000

Ginkophytes

Ginko

1

Cycadophytes

Cycads

130

Gnetophytes

Gnetum, ephedra, and welwitschia

75

Coniferophytes

conifers

600

Flowering plants

250000

Vascular plants Seedless vascular plants

Seed plants Gymnosperms

Angiosperms Anthophytes

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, onecell-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.