The Prokaryotic Domains

I.                    In this class we will employ a modified, Linnaean phylogeny that includes the Domain level taxon.

A.                 Three Domains are generally recognized: The Eubacteria (Bacteria), the Archaea (Archaebacteria), and the Eukarya--proposed by Carl Woese decades ago after he discovered unique RNA signatures in some prokaryotic organisms.

B.                 A summary of the characteristics of the domains is found below.

1.                  The Domains Eubacteria (Bacteria) and Archaea are composed of prokaryotic organisms and share the following characteristics.

a)                  They lack a nucleus and membrane bound organelles.

b)                  They have prokaryotic (70S) ribosomes.

c)                  They control genes via operons.

d)                  Some fix nitrogen.

e)                  They have circular, naked chromosomes and plasmids.

2.                  The Domain Eukarya, includes all eukaryotic organisms, and has the following unique characteristics.

a)                  All are eukaryotes (have a true nucleus and membrane bound organelles).

b)                  They have characteristic plasma membrane phospholipids.

c)                  They have characteristic ribosomes and monocistronic genes.

d)                  They are typically much larger than prokaryotes.

e)                  Chromosomes are linear and composed of chromatin.

f)                    They have membranous organelles.

3.                  The major controversy over Domains is whether the Archaea are indeed distinct and different from the Eubacteria, or whether they should be lumped with the Eubacteria (as they once were, in the Kingdom Monera).

a)                  The Archaea have some unique traits, distinguishing them from both Eubacteria and Eukarya.

(1)               Branched membrane lipids.

(2)               Some membrane lipids span the width of the membrane.

(3)              

Ether groups ( R-C-O-C-R) link membrane lipids to hydrophilic heads instead of ester groups used by Eubacteria and Eukarya.

 

(4)               Some produce methane, and none practice chlorophyll-based photosynthesis.

b)                  The Archaea have some traits in common with Eukarya.

(1)               They lack a class of chemicals known as peptidoglycans in cell walls (present only in the Bacteria).

(2)               They have monocistronic mRNA (mRNA codes for only one protein, rather than several proteins as do the mRNA of Eubacteria).

(3)               The first amino acid encoded by mRNA is methionine (formylmethionine in Eubacteria)

(4)               Their ribosomes are susceptible to diptheria toxins.

(5)               They are resistant to certain antibiotics that are toxic to bacteria.

 

4.                  The table below summarizes the characteristics discussed above.

C.                 Most systematicists consider the Archaea a unique group.

1.                  The fact that the Archaea share traits with both the Eukarya and Eubacteria suggests a common ancestry with both groups.

2.                  Most evolutionists consider Eubacteria to be the first organisms.

a)                  They are thought to have evolved approximately 3.8 billion years ago (bya or ba) in the Archean Eon of the Precambrian time frame.

b)                  Characteristics shared with the Archaea are considered ancestral traits.

3.                  The Archaea are thought to have branched from the Eubacteria

a)                  This branching is estimated to have taken place at least 3 ba, also during the Archean eon.

b)                  Traits being shared with Eukarya are considered derived traits--see diagram below.

4.                  The Eukarya are thought to have branched or formed from the Archaea, with significant contributions from the Eubacteria in the form of organelles.

a)                  This branching is estimated to have occurred 2.5 ba  during the Proterozoic eon of the Precambrian time frame.

b)                  Characteristics unique to Eukarya are considered derived traits.

5.                  The name Archaea means ancient, and originally many felt that Archaea may have been ancestral to both Eubacteria and Eukarya--this theory is not completely dead, although not very well received recently.

6.                 

There are still a significant number of systematicists who consider the Archaea “another prokaryote” that do not deserve their own Domain.

 

D.                 A few additional  comments.

1.                  Prokaryotic systematics has a great deal of work to be done, you are being presented with a timely interpretation, but consider yourself warned, this is an extremely fluid area.

2.                  Recent genetic data is as confusing as it is clarifying as it relates to both the issue of whether the Archaea are a unique Domain, and which Domain is the ancestral group of all life.

3.                  In taxonomies where the Eubacteria and Archaea are not split into separate Domains they are lumped into a clade (Kingdom or Domain) called the Monera or Prokaryota--when you hear these terms they are in reference to prokaryotic organisms without distinction for whether they are Eubacteria or Archaea.

II.                 Prokaryotic systematics is in many ways more difficult than in other types of organisms because of their small size; the difficulty in culturing and isolating pure colonies; and their propensity for swapping genes willy-nilly.

A.                 Morphology has its limitations in Eubacterian and Archaean classification, but there are some terms associated with Moneran shapes.

1.                  Bacilli--rod shaped, example = Escherichia coli (E. coli).

2.                  Cocci--spherical.

a)                  Staphylococci--"clumps" of bacteria like clusters of grapes, example = Staphylococcus aureus.

b)                  Streptococci--"chains" of bacteria, example = Streptococcus sp.

c)                  Diplococci--2 cocci adhered to one another, example = Neisseria gonnorheae.

3.                  Spirilla--spiral shaped bacteria, with external flagella.

4.                  Spirochaetes--spiral shaped with internal flagella, gives them a boring action, example = Treponema pallidum (causative agent of Syphilis), and Lyme’s disease is also caused by a spirochaete.

5.                  Vibrio--comma shaped Monerans

B.                 Biochemistry is much more important in Eubacterian and Archaean classification than morphology.

1.                  One of the most rudimentary biochemical analyses used to identify prokaryotes is by identifying or classifying according to biochemical and structural differences in the cell wall.

2.                  A German, named Gram, devised a stain to differentiate between cell wall characteristics.

a)                  Gram-positive bacteria possess a thick layer of peptidoglycans in their cell wall that retains the dye crystal violet—as a result, they stain a dark purple or blue-black.

b)                  Gram-negative bacteria have a cell wall composed of a thin layer of peptidoglycans and lipids, sandwiched between two plasma membranes—the crystal violet washes out easily and they counter stain a light red or pink color with safranin stain.

c)                  Some bacteria do not readily fit into either category.

3.                  Modes of nutrition are another area of prokaryotic analysis used in prokaryotic classification.

a)                  Heterotrophic (hetero=other, trophic=food or feeding) eubacteria must consume organic molecules, they cannot make their own from inorganic sources.

(1)               They carry out glycolysis for generation of ATP.

(2)               Consumers, in food chains, are heterotrophs.

b)                  Autotrophic (auto=self, trophic=food or feeding) bacteria make their own organic molecules from inorganic sources.

(1)               Photoautotrophic eubacteria use solar energy to construct organic molecules, as we have learned already studying photosynthesis in plants.

(2)               Chemoautotrophic eubacteria use energy from exergonic inorganic chemical reactions to supply the energy to construct organic molecules.

4.                  The toxicity of oxygen is also an important characteristic to consider.

a)                  Obligate aerobes (aero=air or oxygen) require oxygen; their energy pathways are oxygen dependent.

b)                  Obligate anaerobes (an=without, aero=air or oxygen) are oxygen sensitive and have only fermentation (anaerobic) energy pathways.

c)                  Faculative anaerobes can at least tolerate oxygen, and some thrive in either aerobic or anaerobic environments.

5.                  Biochemical features that allow tolerance to extreme environments of heat, cold, pH, salinity, etc are also important.

6.                  Current taxonomies of the Eubacteria, and even the Archaea are based on biochemical phenotypes, which may or may not accurately reflect phylogenetic relationships, as biochemical similarities may have been selected for independently.

7.                  Prokaryotes are identified by growing under specific environmental conditions (nutrient combinations, temperature, acidity, etc), that select for groups of biochemically similar prokaryotes—different kinds of media can also signal the nature of prokaryotic secretions.

C.                 Genetic analysis is another promising method of modern Prokaryotic classification.

1.                  Both DNA and RNA are used for this analysis.

2.                  Genes for ribosomal RNA have been found to be very useful in establishing relationships, as some areas of ribosomal RNA are highly variable.

3.                  A compounding problem in establishing phylogenetic relationships in the Prokaryota is that they readily transfer and exchange genes via plasmids in the process of conjugation.

a)                  These gene transfers occur between highly unrelated prokaryotes, even between Eubacteria and Archaea.

b)                  Genetic analyses, based on relatively few genes, can be misleading because shared genes may be the result of conjugation (gene transfer), transformation (gene assimilation), or viral transduction (viral gene transfer), rather than from a common ancestry.

4.                  Genetic analysis has confirmed that there are many more types of prokaryotes than have been identified.

a)                  Traditional identification of prokaryotes requires the isolation and culturing of prokaryotic organisms.

b)                  These techniques are highly selective--not all prokaryotes thrive in lab conditions, actually, relatively few do so.

c)                  Genetic analyses (DNA fingerprints, PCR) permit the identification of prokaryotes even if they cannot be cultured.

d)                  It is estimated that less than 1% of prokaryotes can be cultured with current techniques.

III.               The Domain Eubacteria (Bacteria) includes the so-called "true" bacteria.

A.                 Characteristics of Eubacteria.

1.                   All are prokaryotes.

2.                  Their genes tend to be “polycistonic” meaning their mRNA codes for more than one protein.

3.                  The eubacteria have characteristic phospholipids, which make up their plasma membranes.

4.                  Eubacteria are important in biogeochemical recycling, disease, and oxygen production (cyanobacteria) to name but a few areas.

5.                  Eubacteria are extremely small, with 5 um a typical size.

6.                  Many Eubacteria (and Archaea for that matter) form “spores” under certain conditions.

a)                  Spores are cells that typically have very thick cell walls and are at least somewhat resistant to desiccation and extreme environmental conditions.

b)                  When favorable conditions return spores germinate to establish a colony.

B.                 The typical Linnaean hierarchy does not work particularly well with the Eubacteria, especially at the species level, several Eubacterial clades (Kingdoms)  are described below.

1.                  Proteobacteria-- a diverse clade that includes the following (Divisions).

a)                  Purple sulfur bacteria—sulfur using photoautotrophs important in sulfur cycling in nature.

b)                  Nitrogen fixing bacteria—includes Rhizobium, a soil bacterium that fixes atmospheric nitrogen into ammonia, it and others responsible for cycling of nitrogen in nature.

c)                  Gram-negative bacteria--many common heterotrophic bacteria including famous pathogens including Vibrio (diarrhea), and Yersinia. (Plague), Escherichia coli (E. coli).

2.                  Cyanobacteria (Cyanota)--the so-called blue-green algae, they are photosynthetic bacteria, producing oxygen, they contain sheets of plasma membranes that contain photosystems, they utilize chlorophyll-a, just like plants, but contain a phycolibin pigments that are not found in plant chloroplasts, form heterocysts that are nitrogen fixing, form akinetes (spores), and heterocysts (N-fixing cells), Prochloronta a subclade that is ancestral to plant chloroplasts.

3.                  Spirochaeta--long spiral, flagella within cell wall, decomposers and pathogens, examples: Treponema, Borrelia.

4.                  Firmicutes—another diverse clade (Kingdom) composed of the following (Divisions).

a)                  Mycoplasmas--smallest bacteria (0.2 um), no cell wall, obligate parasites, amoeboid and colonial at times, examples: Mycoplasma.

b)                  Rickettsias (Chlamydias)--very small, possess cell wall, obligate parasites, examples: Chlamydia, Rickettsia.

c)                  Gram-positive bacteria--also many common bacteria, includes the endospore forming bacteria, examples: Clostridium (tetanus, botulism), Bacillus.

d)                  Actinomycetes--most non-motile, decomposers, some parasites, examples: Streptomyces, Actinomyces.

5.                  Thermophilic bacteria--tolerate extreme heat, often found with Archaea, example: Thermus aquaticus, source of Taq polymerase used in PCR gene amplification, found in Yellowstone thermal pool.

6.                  Myxobacteria-- rod-shaped "gliding" bacteria, mostly decomposers. Examples: Myxococcus, Chondromyces.

IV.              The members of the Domain Archaea are often described as “extremeophiles” meaning found only in extreme environments of temperature, pH, and salinity.

A.                 Two clades (Kingdoms) of Archaea are generally recognized

1.                  The Crenarchaeota is composed of the following clades (Divisions).

a)                  Hyperthermophiles--are thermophilic and most also acidophilic, typically live in hot sulfur springs or deep ocean vents, can tolerate pH to 0.9 yet maintain neutral cytoplasmic pH, example: Sulfobus.

b)                  Extreme Halophiles--salty environments, many contain carotenoids and have reddish-orange color, common in many inland seas (Salton Sea, Dead Sea), example: Halobacterium.

c)                  Thermoplasma--thermophilic and acidophilic, lack cell walls, have been found in coal deposits, genome only 1100 kilobase pairs (200 genes or less?).

2.                  The Euryarchaeota is composed of a single clade (Division), the Methanogens, which are obligate anaerobes that produce methane by reducing carbon dioxide, some live in animal guts (yes yours too) producing flatulence (yes it is flammable), example: Methanopyrus.

B.                 Extremeophiles are investigated for potential economic value by copying characteristics of their enzymes for use in industry.

1.                  Though once thought restricted to extreme environments it is becoming obvious that the Archaea are found in all environments, just like Bacteria.

2.                  As mentioned previously, prokaryotic taxonomy is extremely fluid, and will change significantly in the next decade.

V.                 Viruses are generally ignored taxonomically, thought to have evolved after prokaryotes.

A.                 As we have discussed, viruses are a bit of an enigma, and are often discussed as organisms, without being given the courtesy of a place in a taxon.

B.                 Physical structures

1.                  Nucleic acid--the genetic material either DNA or RNA.

a)                  RNA may be positive sense = RNA that can be used directly by ribosomes (of host) to make proteins that will make new viruses.

b)                  RNA may be negative sense = RNA that cannot be used by ribosome to make protein.  Negative sense strand is used to make a positive sense strand by an accompanying enzyme (transcriptase).

c)                  RNA is used as a template to make DNA strands (retroviruses)

2.                  Capsid--encloses the nucleic acid, composed of protein(s).

3.                  Envelope--some viruses have a bilipid membrane enclosing the capsid, often derived from host (virus is "naked" if lacks envelope).

C.                 Viruses lack all other cellular organelles, enzymes etc, and will use those of the host cell to make new viruses (a few viruses do have one or two enzymes, but are not activated until within a cell).

D.                 Many viruses capable of lysogenic phase (DNA incorporated into hosts) and lytic phase (host cell destroyed).

E.                  “Clades” of viruses are listed below.

1.                  RNA viruses (shaded viruses for you information).

a)                  Picornaviruses--naked, single positive sense strand of RNA, no enzymes, and two types.

b)                  Enterovirues--enter through the intestinal lining can infect all tissues including muscle and nervous, includes polioviruses.

c)                  Rhinoviruses--enter and destroy cells of upper respiratory tract, cause common cold.

d)                  Togaviruses--enveloped, single positive sense strand of RNA, no enzymes, cause yellow fever, rubella, and some encephalitis.

e)                  Paramyxoviruses--enveloped, single strand of negative sense RNA, transcriptase enzyme, cause mumps, measles, croup, viral pneumonia.

f)                    Rhabdoviruses--same characteristics as paramyxoviruses, but capsid and envelope different shape, mainly infect insects and plants, but do cause rabies in humans.

g)                  Orthomyxoviruses--enveloped, several single strands of negative sense RNA, cause influenzas.

h)                  Bunyaviruses--have the same characters as orthomyxoviruses, envelope derived from endoplasmic reticulum, often endemic in rodents and passed to humans by insects, cause California encephalitis.

i)                    Arena viruses--same as Bunyaviruses but envelope derived from cell membrane, causes some hemorrhagic fevers in which blood vessels rupture in skin, mucous membranes, and internal organs.

j)                    Reoviruses--double capsid, no envelope, one positive and one negative sense RNA strand, cause gastrointestinal and upper respiratory infections.

k)                  Retroviruses--envelope, two positive sense RNA strands, enzyme reverse transcriptase which makes DNA from the RNA strands which may then be incorporated into host chromosomes (provirus, lysogenic phase), generally invade T lymphocytes, causes HTLV infections (tumors, leukemia), and HIV infections (AIDS).

2.                  DNA viruses.

a)                  Adenoviruses--naked; double stranded, linear, DNA; causes severe diarrhea in infants and children, other infections when immune system suppressed, also being used in genetic engineering efforts.

b)                  Herpes viruses--envelope; double stranded, linear DNA; causes oral and genital herpes, chickenpox, shingles, encephalitis, birth defects, infectious mononucleosis.

c)                  Poxviruses--like herpes viruses, though larger; causes smallpox, cowpox.

d)                  Papovaviruses--naked; double stranded circular DNA; causes benign and malignant warts.

e)                  Parvoviruses--naked; single stranded, linear DNA; some require co infection with adenoviruses; causes roseola in children, aggravates sickle cell anemia, canine parvo (gastrointeritis).

F.                  Related topics.

1.                  Viroid-- is a strand of free RNA, without envelope or capsid, transmittable, possibly derived from viruses.  Active in some plant diseases.

2.                  Prions--still theoretical infectious protein.

a)                  Causes Scrapie in sheep, BSE (Bovine Spongiform Encephalopathy) in cows, CWD (Chronic Wasting Disease) in elk and deer, and Crutzfeld-Jacob Disease in humans.

b)                  All cause “holes” to form in brain.

c)                  Two versions of a protein, normal and abnormal.

(1)               Abnormal version may induce normal proteins to refold into abnormal form.

(2)               Abnormal form causes neurofibrillary tangles and brain plaques.

(3)               Neuron death results, and immune cells clean up mess.

d)                  Prions hard to destroy, “immortal,” potentially huge health threat.

e)                  Cattle infected from feed containing sheep “parts,” cows may have infected humans.

I.                    By approximately 2.5 ba, the Eukarya had evolved.

A.                 The Eukarya probably share a common ancestor with the Archaea, because of the characteristics they share.

1.                  They lack a class of chemicals known as peptidoglycans in cell walls (present only in the Bacteria).

2.                  They have monocistronic mRNA (mRNA codes for only one protein, rather than several proteins as do the mRNA of Eubacteria).

3.                  The first amino acid encoded by mRNA is methionine (formylmethionine in Bacteria)

4.                  Their ribosomes are susceptible to diptheria toxins.

5.                  They are resistant to certain antibiotics that are toxic to bacteria.

B.                 Eukarya not only evolved from prokaryotic ancestors, but some structures certainly resulted from endocytoisis of, and symbiosis with prokaryotes.

1.                  Structures like endoplasmic reticulum, the nuclear envelope, golgi bodies, microsomes, lysosomes, vacuoles, and vesicles are products of eukaryotic evolution.

2.                  Mitochondria and chloroplasts are remnants of prokaryotic symbionts that have taken mutualism to an extreme.

a)                  Both mitochondria and chloroplasts have a double membrane structure, prokaryotic ribosomes, their own chromosomes and plasmids, divide independently of the cell, and have structural, chemical and genetic signatures that link them to existing prokaryotes.

(1)               The mitochondria are closely related to members of the purple sulfur bacterial clade.

(2)               Chloroplasts are closely related to members of the Prochloronta bacterial clade.

b)                  There is precedent for the evolution of symbiotic prokaryotes developing mutualistic relationships with eukaryotes--bacterial symbionts in protozoa in guts of termites, sheep, cows and other ungulates.

3.                  The origin of eukaryotic flagella is highly debatable.

a)                  Some think the flagellum evolved from a symbiotic spirochaete.

b)                  Others feel the flagellum is not derived from prokaryotes but evolved independently.

II.                 The Protista is traditionally viewed as a Kingdom (within the Eukarya).

A.                 The Protista, from a phylogenetic perspective, is highly problematic.

1.                  The Protista as a clade is not monophyletic--it is really an artificial construct, traditionally a “dumping ground” for eukaryotic organisms whose ancestry is uncertain.

2.                  Some clades within the Protista are certainly related, but members of the Protista evolved separately from eukaryotic ancestors.

3.                  Modern taxonomies generally eliminate the Protista as a Kingdom and elevate what were Protist Divisions to Kingdoms, or novel Kingdoms have been created and the Protist Divisions reorganized within them.

B.                 The Protista are generally defined as having the following characteristics: eukaryotic, most are unicellular, some are colonial, the multicellular forms lack strong tissue development, they live in aqueous, marine, or extremely humid environments, and some form protective spores.

1.                  Tissues are groups of cells specialized for a particular function--they are specialized cells.

2.                  Colonial organisms are composed of cells that have the capacity to live individually, and do so in the course of their life cycle.

3.                  Multicellular organisms may be composed of undifferentiated cells, but their cells do not live individually.

C.                 The reality is that just as the early evolution of life is highly muddled, so too is the early evolution of eukaryotic life--we are not certain at this point of what kind interactions produced the still extant Eukarya, especially since microfossils are hard to come by, and are not particularly informative.

D.                 Because the Protists are not monophyletic a variety of reproductive life histories are practiced--we will consider these when relevant.

E.                  The term, Protist, then will be used as a descriptive term to describe the Divisions of life forms often described as Protozoa, Fungi-like Protists, and Algae.

1.                  The Protozoa are animal-like, unicellular (although some may be colonial), and heterotrophic Protists.

2.                  The Fungi-like Protists are clades of organisms that have some characteristics of the fungal clade, and were at one time actually classified as Fungi.

3.                  The Algae are nonplant; chlorophyll based photosynthetic eukaryotes that live in fresh water or marine habitats.

III.               A number of Protist clades will be discussed below.  These will be considered Linnaean Kingdoms within the Domain Eukarya.

A.                 The (Kingdom) Diplomonada are spore-forming flagellates that lack mitochondria, includes the genus, Giardia, which contaminates streams, rivers, and lakes throughout the Western Hemisphere, causing a severe diarrhea.

B.                 The (Kingdom) Trichomonada are small, oval or round Protozoa, which also lack mitochondria.

1.                  They have several flagella at one end, a small undulating membrane (described below), and an axoneme.

2.                  The genus, Trichomonas, causes urinary tract infections in men and women, and vaginitis in women.

C.                 The (Kingdom) Kinetoplastida have a single large mitochondrion that includes a structure called a kinetoplast.

1.                  The kinetoplast contains DNA and proteins.

2.                  Trypanosomes are Kinetoplastids that have a single flagellum that runs the length of the cell, encased within the cell membrane.

3.                  When the flagellum beats it creates an “undulating membrane” characteristic of the clade.

4.                  The genus Trypanosoma causes sleeping sickness in Africa, and Chagas Disease in Central and South America.

5.                  Trypanosomes typically employ insect vectors as intermediate hosts, e.g. the tse-tse fly carries sleeping sickness and kissing bugs transmit Chagas Disease.

D.                 The (Kingdom) Hypermastigophora have numerous (dozens and dozens) of flagella, rather than the few typical of most flagellates.

1.                  Members of the genus, Trichonympha, live in gut of cows, sheep, and termites, digesting cellulose for their hosts in a mutualistic relationship.

2.                  The mutualism is extended because bacteria living within the Trichonympha actually digest cellulose, benefiting both the Protozoan and Vertebrate hosts.

E.                  The term Amoeba refers to protozoans that locomote via amoeboid movement--extending psuedopods, and crawling over a surface.

1.                  Evidence suggests the membrane rolls like a tank tread.

2.                  The cytoplasm contains contractile proteins (the same as are found in our muscles) that act to push (or pull) the cell along.

a)                  Cytosol is the cytoplasm in an uncontracted state.

b)                  Cytogel is the cytoplasm in a contracted state.

c)                  Cytogel changes to cytosol at the posterior of the cell, flows to the anterior end of the pseudopod, and converts back to cytogel.

3.                  There are free living, parasitic, aquatic and marine amoebas.

4.                  Some Amoeboid clades (Kingdoms) include the following.

a)                  The (Kingdom) Rhizopoda are the typical amoebas.

(1)               The genera Ameoba, and Chaos are free-living aquatic examples.

(2)               The genera Naeglaria is a brain parasite that can enter via the nasal mucous membranes and Entamoeba causes amoebic dysentery and is ingested.

b)                  The (Kingdom) Foraminifera are marine plankton that have a calcium carbonate “test” (shell) external to the cell membrane.

(1)               Readily form fossils; foram skeletons date time periods.

(2)               Form limestone deposits.

c)                  The (Kingdom) Actinopoda have thin stiff pseudopods with microtubular endoskeletons.

(1)               The actinopods function in feeding and locomotion.

(2)               The Actinopoda are found in marine and freshwater plankton.

(3)               There are two Actinopod subclades (Divisions)

(a)                The Radiolaria are exclusively marine, have an internal shell of silicon to support pseudopods and  “body.”

(b)               The Heliozoa are freshwater, lack intricate silicon endoskeleton.

F.                  The (Kingdom) Ciliophora are ciliated protozoans.

1.                  All members have cilia which are identical to flagella in cross section ("9+2") but much shorter, and typically more numerous.

2.                  Ciliates have two morphologically different nuclei.

a)                  Most have several micronuclei, and a single macronucleus that is polyploid.

b)                  Ciliates reproduce asexually by mitosis, and sexually as described below.

(1)               Two ciliates associate and their pellicle (rigid cell membrane) will fuse.

(2)               The macronucleus and all but one micronucleus disintegrate.

(3)               The remaining micronucleus will undergo meiosis, producing four micronuclei, of which three will disintegrate.

(4)               The remaining micronucleus will undergo mitosis.

(5)               The ciliates exchange one micronucleus with one another  (in a process called conjugation).

(6)               The ciliates dissociate.

(7)               The micronuclei fuse together creating a diploid nucleus in each ciliate.

(8)               The diploid micronucleus undergoes mitosis making multiple copies.

(9)               Several of the micronuclei will fuse to form a polyploid macronucleus.

(10)           The macronucleus appears to run the day-to-day activities of the ciliate, with the micronuclei crucial for sexual reproduction.

3.                  The Ciliates are a diverse and complex group; most are free living in marine or aquatic habitats.

4.                  Examples include the genera Paramecium, Stentor, Vorticella, etc.

G.                 The (Kingdom) Opalinida are also ciliated protozoa.

1.                  Members are similar to ciliates in that they have cilia, but they have only micronuclei.

2.                  Have multiple nuclei (multinucleate) that are iridescent when viewed under the light microscope making them look like jewels--hence the name opalinids (opal-like).

3.                  Most are parasites of amphibian intestines.

H.                 The (Kingdom) Apicomplexa are protozoa that lack flagella.

1.                  All members are obligate parasites, and lack motility (no pseudopodia, cilia, flagella, etc.) in parts of their life cycles.

2.                  Most form "spores", or resistant capsular forms that enable them to survive unfavorable periods--the Apicomplexans are sometimes called the Sporozoa.

3.                  Members often demonstrate complex life cycles, and modes of transmission from one host to another.

4.                  Example: Plasmodium the causative agent of malaria, a disease of the blood, noted for its cyclic and intense fevers--the life cycle is listed below.

a)                  The Anophales mosquito ingests human blood containing haploid gametocytes, floating free in the blood plasma.

b)                  In the mosquito gut, the gametocytes develop into gametes and fuse to form a diploid zygote.

c)                  The zygote burrows into tissue around the gut and forms a cyst called a sporocyst.

d)                  Within the cyst schizogony occurs, a method of mitotic cell division that yields many small cells.

e)                  These cells, called sporozoites, are the infective stage to humans.

f)                    The sporozoites break out of the sporocyst and migrate to the salivary glands.

g)                  When the mosquito feeds on a human it clears its proboscis injecting sporozoites into the bloodstream.

h)                  Sporozoites invade liver cells (hepatocytes).

i)                    Within the liver cells they undergo schizogony, forming cells called merozoites.

j)                    Merozoites break out of the liver cells (destroying them) and infect RBC’s.

k)                  The merozoites undergo schizogony within the RBC’s destroying them when they break out.

l)                    The infection grows exponentially with each cycle and the cycle is regular and synchronized (every 24, 48, 72 hours depending on the species)--causing periods of intense fever and discomfort (when the merozoites break out of RBC’s) followed by periods of recovery (while merozoites are reproducing within the RBC’s).

m)                Some merozoites will undergo meiosis forming gametocytes that continue the cycle in the mosquito.

n)                  The disease causes jaundice, hepatitis, and severe anemia, and is fatal if not checked by drugs or the immune system.

o)                  Numerous drug resistant forms now exist, so your best protection is insect repellant and mosquito netting when sleeping.

I.                    The (Kingdom) Choanoflagellida are flagellated protozoa.

1.                  Have a collar-like structure supported by microtubules around flagella.

2.                  Most form colonies and filter feed by catching organic matter in collar.

3.                  Are considered the ancestral group to the Metazoa (Animals).

J.                   There are three clades (Kingdoms) of slime molds, considered fungi-like Protists.

1.                  Slime molds have the following characteristics.

a)                  They are motile (something like large amoebae).

b)                  They are detritivores that ingest food by endocytosis.

c)                  They form spores on elaborate “fruiting bodies.”

d)                  They change forms many times, forming aggregates of cells at times, and cells dissociate at times.

2.                  The (Kingdom) Myxomycota.

a)                  The Myxomycota are acellular slime molds.

b)                  The Myxomycota life history includes the following.

(1)               The myxomycota form a diploid plasmodium, in what is the “vegetative” or non-reproductive phase of the organism’s life cycle.

(a)                The plasmodium is described as a syncytium or coenocytic mass in which the internal walls and membranes break down forming a huge cytoplasmic mass with multiple diploid nuclei.

(b)               It is basically a large mass of cytoplasm encapsulated by a plasma membrane.

(c)                The cytoplasm streams much like that of an amoeba--streaming is the work of contractile proteins.

(d)               The plasmodium streams along forest floors, feeding on decaying vegetation or other detritus, as well as fungi, and bacteria in the soil.

(2)               When conditions change the plasmodium converts into one of two structures.

(a)                It may form a sclerotium--basically a dehydrated plasmodium that will reform a plasmodium when rehydrated.

(b)               It may form a fruiting structure.

(i)                  Cells form.

(ii)                These form a structure which rises above the plasmodium

(iii)               So-called sporangia form, and sporangial cells undergo meiosis to form haploid spores with resistant cell walls.

(iv)              Spores are disseminated.

(v)                Spores develop into amoeboid haploid cells called swarm cells that feed and move independently--they divide mitotically.

(vi)              Swarm cells may fuse, acting as gametes to form a zygote.

(vii)             The zygote divides, forming a plasmodium, completing the life cycle.

(3)               Example: the genus Physarum.

3.                  The (Kingdom) Dictyostelida.

a)                  The Dictyostelida are one of two types of cellular slime molds.

b)                  The life cycle is as follows.

(1)               Large numbers of individual, haploid, amoeboid cells, called myxamoebas, are the vegetative form of the cellular slime molds--they migrate and ingest detritus, bacteria, and fungi.

(2)               When conditions are unfavorable the myxamoebas aggregate to form a large mass called a pseudoplasmodium.

(a)                Cells retain their individual identity in the pseudoplasmodium; they do not form a syncytium.

(b)               Myxamoebas from pseudoplasmodia in response to the production of cAMP (cyclic AMP), caused by unfavorable conditions.

(3)               The cells of the pseudoplasmodium form a fruiting structure.

(4)               Haploid spores are formed and released; these germinate to produce myxamoebas when conditions are again favorable.

(5)               A sexual cycle may also occur.

(a)                Two haploid myxamoebas may fuse form a zygote.

(b)               The zygote forms a spore or capsule, within which meiosis occurs.

(c)                It germinates to yield haploid myxamoebas.

c)                  Example: the genus Dictyostelium.

4.                  The (Kingdom) Acrasida are another group of cellular slime molds that do not use cAMP as a signal for pseudoplasmodial formation.

K.                The (Kingdom) Oomycota are also fungi-like Protists.

1.                  The Oomycota are known as water molds and downy mildews.

2.                  They form filaments called hyphae, and the mass of hyphae is called a mycelium.

3.                  The hyphae are coenocytic, i.e. there are no internal separations, and the cell walls are composed of cellulose without chitin.

4.                  Both aquatic and terrestrial forms, and feed by absorption of detritus, or act as parasites.

5.                  Will form diploid flagellated zoospores under the proper conditions.

6.                  Life cycle.

a)                  Diploid mycelia are of + and - types.

b)                  The hyphae of the mycelia may develop sporangia that will produce motile zoospores that disseminate by swimming.

c)                  These zoospores will germinate into new diploid hyphae and produce new mycelia in an asexual reproduction.

d)                  Sexual reproduction proceeds as follows.

(1)               Hyphae of the + type grows towards structures called oogonia formed by hyphae of the - type.

(a)                The + hypae form antheridia around oogonia.

(b)               Antheridia undergo meiosis to produce haploid nuclei that will act as “male” gametes.

(c)                “Female” gametangia are called oogonia and produce large haploid, non-motile gametes (ova), via meiosis.

(2)               The antheridial hyphae fuse with the ova of the oogonia and the nuclei fuse forming zygotes.

(3)               The zygotes develop into oospores that are released from the oogonium.

(4)               The oospores germinate into diploid hyphae (+ or -).

7.                  Examples: Saprolegnia forms mold on dead fish or insects, Phytophthora infestans is a parasite that caused the potato famine in Ireland between 1845-47.

L.                  The (Kingdom) Euglenophyta are faculative heterotrophic algae.

1.                  Unicellular, flagellated green algae.

2.                  Possess flagella, in past were classified as flagellates, or within the Chlorophyta.

3.                  Cell walls do not contain cellulose.

4.                  Though they have chloroplasts are faculative heterotrophs, meaning they can live for extended periods without light.

5.                  They have a light sensitive organelle called stigma.

6.                  Are common fresh-water phytoplankton.

7.                  Example: the genus Euglena.

M.               The (Kingdom) Chrysophyta, common name the golden (yellow) algae.

1.                  Unicellular, some colonial or filamentous, with two flagella of unequal lengths.

2.                  The group includes golden-brown algae, and yellow-brown algae.

3.                  Cell wall composed of pectin and silicon rather than cellulose.

4.                  They store oils, rather than starch (as plants do) as photosynthetic storage products.

5.                  Even though yellowish in color, they, like all algae have chlorophyll-a, in addition to carotenoid accessory pigments.

6.                  Desmids are are an example of a Chrysophytan.

7.                  Most are unicellular, forming a large portion of marine and freshwater plankton--an important part of the 1st trophic level in marine ecosystems.

N.                The (Kingdom) Bacillariophyta, common name, Diatoms, are closely related to the Chrysophyta.

1.                  Diatoms have a shell composed of two halves that fit together like a petri plate.

2.                  When diatoms mitotically divide the diploid daughter cells each get one half of the shell.

3.                  It secretes the other half, but it will always grow a “bottom half” to the shell it inherited.

4.                  As a result, the cells get progressively smaller.

5.                  When diatoms reach a minimum size, it triggers the nucleus to undergo meiosis, releasing haploid gametes into the water.

6.                  The gametes fuse forming a zygote, which grows to maximal size and secretes two new halves forming a new large silicon test (shell), starting the cycle over again.

O.                The (Kingdom) Pyrrophyta, common name fire algae.

1.                  Unicellular flagellates.

2.                  This clade includes the Dinoflagellates = "spinning flagellates".

3.                  Possess two flagella in grooves (longitudinal and transverse-polar and equatorial), makes the cell spin as it swims.

4.                  Cell wall contains cellulose.

5.                  Contain chlorophyll a and red pigments--responsible for the "red tides" of summer months--many also secrete toxins.

6.                  Mollusks (clams, etc.), and other filter feeders accumulate the toxins by feeding on the dinoflagellates, and in the process become toxic to humans.

7.                  Many forms also bioluminescent.

P.                  The (Kingdom) Phaeophyta, common name, brown algae.

1.                  Multicellular algae, includes the largest algae in the world, coastal brown kelps are members of the clade.

2.                  Plastids contain fucoxanthin and phycobilin and carotenoid pigments.

3.                  Store excess energy as oils.

4.                  Cell walls contain alginic acid.

a)                  Kelp is harvested for their alginic acid.

b)                  Is used as a colloidal emulsifier in cosmetics and ice cream.

5.                  Brown kelp among fastest growing organisms in the world.

6.                  Most brown kelp are anisogamous, heteromorphic, and sporophyte dominant.

7.                  Examples: Sargassus (free floating), Macrocystis (coastal brown kelp).

8.                  The Phaeophyta are one of three Kingdoms of Algae (including Rhodophyta and Chlorophyta) that include large, multicellular seaweeds.

a)                  They are truly multicellular and not colonial.

b)                  They can be extremely large and show structural specialization although cell specialization is not pronounced, when compared to plants.

(1)               The algal “plant” is called a thallus.

(2)               The holdfast anchors the thallus to a substrate, typically rock.

(3)               The stipe is the “stem” of the thallus.

(4)               The blade is the “leaf” of the thallus.

(5)               Many blades have pneumatophores (gas bladders) that support the thallus.

Q.                The (Kingdom) Rhodophyta, common name, red algae.

1.                  Mostly multicellular, some filamentous algae.

2.                  Plastids contain phycoerythrin, phycocyanin, and carotenoids.

3.                  Store energy as Floridian starch (highly branched).

4.                  No motile gametes or spores produced.

5.                  Cell wall contains a mucilagenous polysaccharide (composed in part of galactose sulfate) that forms agar.

6.                  Red algae harvested for agar--used in microbiology and food industry.

7.                  Some species parasitic on other red algae.

8.                  Are considered ancestral to Chlorophyta.

R.                 The (Kingdom) Chlorophyta, common name, the green algae, form a monophyletic clade with the plants.

1.                  The Chlorophyta and plants store starch.

2.                  The Chlorophyta and plant plastids contain the same photosynthetic pigments: chlorophyll-a and b, xanthophylls, beta-carotene, and other characteristic carotenoids.

3.                  The Chlorophyta and plants have cellulose cell walls.

4.                  Includes unicellular (Chlamydomonas), colonial (Volvox) and multicellular (Ulva, Ulothrix) genera.

5.                  Variety of life cycles exhibited, although at least one species demonstrates an extreme form of anisogamy called oogamy--flagellated “sperm” and nonmotile large “ovum” (same as in plants).

6.                  The life cycle of the filamentous green alga, Spirogyra, is somewhat atypical of the Kingdom, but is easily observable.

a)                  Filaments are haploid  + and – types.

b)                  When opposite types contact one another a conjugation tube forms.

c)                  The cytoplasm of the + type streams into the – cell, and encapsulates.

d)                  The nuclei fuse forming a zygote.

e)                  The zygote eventually drops to the bottom.

f)                    The zygote undergoes meiosis, yielding haploid cells.

g)                  The haploid cells grow into new filaments.

IV.              I have not organized the Protist clades evolutionarily within subclades because most of the relationships are nebulous at this time, in my opinion.  Having said that, below is listed what is currently considered the most likely relationships, from most ancestral to most recent, with some clades I have previously described as Kingdoms, organized within new Kingdoms as Divisions.

A.                 Kingdom Archaezoa—lack mitochondria.

1.                  Division Diplomonada.

2.                  Division Trichomonada.

B.                 Kingdom Euglenozoa—possess and anterior pocket, from which two flagella protrude.

1.                  Division Euglenophyta.

2.                  Division Kinetoplastida.

C.                 Kingdom Alveolata—membrane-bound cavities under cell membrane.

1.                  DivisionPyrrophyta.

2.                  Division Apicomplexa.

3.                  Division Ciliophora.

D.                 Kingdom Stramenopila—characteristic flagella with hair-like projections (when present).

1.                  Division Bacillariophyta.

2.                  Division Chrysophyta.

3.                  Division Phaeophyta.

4.                  Division Oomycota.

E.                  The amoeboid Kingdoms are sometimes organized as Divisions within a Kingdom called the Sarcodina.

F.                  The flagellated Kingdoms are sometimes organized as Divisions with a Kingdom called the Mastigophora.

G.                 We have not considered all of the Protist clades (Kingdoms).

I.                    The Fungi are a monophyletic clade of organisms that are generally recognized as a Kingdom in the Linnaean hierarchy and have the following characteristics.

A.                 All Fungi are absorptive heterotrophs, meaning they absorb already decayed matter or secrete digestive enzymes to break down tissue extracellularly; they do not endocytose and digest internally.

B.                 The Fungi are more closely related to Animalia that Plantae.

C.                 The Fungi evolved from flagellated ancestors in the Proterozoic eon of the Precambrian time frame approximately 1.5 ba.

D.                 Almost all (yeasts are an exception) are multicellular, growing filaments called hyphae that form a mycelium.

E.                  The hyphae are typically coenocytic, with incomplete septa (internal cell walls).

F.                  All fungi have cell walls that contain at least some chitin, a nitrogenous polysaccharide.

G.                 Almost all fungi exhibit a three-stage life cycle that involves a haploid stage, a dikaryon stage, and a diploid stage.

1.                  Haploid mycelia are of + and - types.

2.                  Positive hyphal cells fuse with negative hyphal cells resulting in a dikaryon--the dikaryon cells contain two, unfused, genetically different, haploid nuclei.

3.                  The dikaryon may produce hyphae and a dikaryotic mycelium.

4.                  The haploid nuclei will eventually fuse in some cells forming a zygote.

5.                  The zygote will undergo meiosis producing haploid spores that are released and will germinate to produce new haploid hyphae and mycelia.

6.                  Spores may be formed in any or all of these stages.

H.                 Fungi have a variety of ecological roles.

1.                  Most Fungi are saprobes or detritivores (feed on dead matter); they are one of the major detritivores in nature, and help recycle nutrients in the process of bioremediation.

2.                  There are many fungal parasites of animals, plants, and other organisms.

3.                  A few fungi are predatory capturing and feeding on nematodes (roundworms) or Protists.

4.                  Some fungi form symbiotic relationships.

a)                  Nitrogen fixing bacteria (Rhizobium) and plant roots allow plants to fix nitrogen.

b)                  Mycorrhizae are fungi that associate with plant roots.

(1)               The mycorrhizae absorb phosphates, nitrates or other nutrients from the soil and transfer to the root hair; some also secrete plant growth hormones.

(2)               The mycorrhizae absorb sugars from the plant root (it may actively tap into the plant phloem).

(3)               Some are ectomycorrhizae and others endomycorrhizae.

c)                  Lichens were once thought to be organisms, but are symbiotic relationships between unicellular algae (or cyanobacteria) and fungi.

(1)               Lichens grow in austere environments, such as on exposed rock or dead wood.

(2)               Fungi secrete enzymes to break down rock or wood and absorb minerals or nutrients to be shared with the algal cells.

(3)               The algae photosynthesize generating sugars for themselves and the fungi.

(4)               The fungi are typically external to the algae, this is convergent to leaf structure in that the photosynthetic cells are internal to those that are not.

(5)               The fungal component is typically an ascomycota, although basidiomycota and deuteromycota occur (only one zygomycota is known in lichens).

(6)               The algal component is typically a unicellular chlorophytan, although cyanobacteria are common.

(7)               The relationship is traditionally viewed as mutualistic but actually the fungi may be parasitic.

(8)               They typically reproduce by the formation of soredia.

(a)                Soredia are algal or cyanobacterial cells surrounded by hyphae.

(b)               The soredia are carried away by wind or water.

(9)               In most lichens the fungi will form characteristic sporangia and spores (ascosporidia, basidia).

II.                 Fungal clades (Phyla (Divisions)) are discussed below.

A.                 The Chytridiomycota (chytr = flower pot, mycota = mold)--the Chytrids.

1.                  Most ancient group of fungi, extremely diverse--saprobes, parasites, marine, freshwater, and soil varieties.

2.                  Life cycle of Allomyces.

a)                  A haploid zoospore germinates on detritus forming a small hypha.

b)                  The end enlarges forming a gametangium that will produce either male or female gametes--both are flagellated.

c)                  The flagellated gametes are released, male gametes swim to female gametes and they fuse (male gametes are smaller), forming a dikaryon.

d)                  The nuclei of the dikaryon fuse, forming a zygote.

e)                  The zygote develops into a spherical sporangium that may have radiating hypae.

f)                    The sporangium produces diploid zoospores that are disseminated and produce more of the sporangia.

g)                  Some of the sporangia develop into thick walled structures called “resting sporangia” that are resistant to environmental stress.

h)                  When favorable conditions return sporangial cells undergo meiosis producing haploid zoospores, starting the cycle over again.

B.                 The Zygomycota -- the zygospore forming fungi.

1.                  The Zygomycota are characterized by formation of heavy walled, black, zygospores.

2.                  Life cycle of Rhizopus stolonifer, black bread mold.

a)                  Haploid hyphae of a mycelium are coenocytic.

b)                  Hyphae may asexually reproduce by forming terminal sporangia at the end of hyphae--these produce spores, which are disseminated and germinate into new hyphae and form and new mycelium (the spores are nonmotile).

c)                  Sexual reproduction is triggered when + and - hyphae grow near one another.

d)                  Gametangia form at the tips of the hyphae; the gametes fuse forming a diploid zygote.

e)                  The zygote forms a heavy wall and is highly resistant to environmental stress—it is now considered a zygosporangium.

f)                    Eventually the zygosporangium undergoes meiosis, forming numerous haploid “zygospores” that are released from zygosporangium when it ruptures.

g)                  The spores germinate to produce new + or - hyphae and new mycelium.

h)                  The hyphae may also form sporangia and spores in an asexual cycle.

C.                 The Basidiomycota -- the club fungi.

1.                  The Basidiomycota includes mushrooms (Agaricus, Aminita), shelf (bracket) fungi, rusts (Puccinia graminis), smuts, and puffballs.

2.                  A mushroom life cycle.

a)                  + and - haploid hyphae in the soil grow together and produce dikaryotic cells.

b)                  A dikaryotic mycelium will develop--this is a highly compact mycelium (basidiocarp) and will develop into the stipe (stalk) and pileus (cap) of the mushroom.

c)                  In the cap, gills develop, and dikaryotic cells called basidia (club-shaped) form at the end of hyphae.

d)                  Within the basidia the haploid nuclei fuse forming a zygote, which immediately undergoes meiosis.

e)                  The resulting haploid nuclei are borne within spores on the tip of the basidium, and are called basidiospores.

f)                    The haploid basidiospores are disseminated and germinate into + or - hyphae, starting the cycle over again.

3.                  Basidiomycete life cycles can be very complex, with several types of spores being produced, and asexual cycles incorporated as well.

4.                  Some rusts form haploid, diploid, and dikaryotic mycelia and spores.

D.                 The Ascomycota--the sac fungi.

1.                  The Ascomycota includes yeasts, morels, truffels, and cup fungi.

2.                  All Ascomycota produce spores within a sac like structure called an ascus.

3.                  There are two clades (Classes) of Ascomycota.

a)                  The Hemiascomycota are primarily unicellular Ascomycota known as yeasts, an example is Saccharomyces cerevisiae used in baking and brewing.

(1)               Yeasts asexually reproduce by budding.

(2)               Haploid yeasts can fuse with other yeasts of a different mating type (+ and -).

(3)               The nuclei fuse forming a zygote.

(4)               The zygote undergoes meiosis producing four or eight spores within the cell, which serves as the ascus (sac).

b)                  The Euascomycota include all other Ascomycota.

(1)               The Euascomycota hyphae are haploid.

(2)               They may form conidia (or conidiophores) at the ends of the hyphae, which produce conidiospores (chains of spores, unprotected by a sporangium).

(3)               Conidospores germinate to produce new hypae.

(4)               Hyphae may form a fruiting structure (as in the cup fungi).

(5)               + hyphal cells fuse with - hyphal cells to form dikaryotic cells which grow into dikaryotic hyphae.

(6)               When asci develop, the nuclei fuse, forming a zygote, which immediately undergoes meiosis.

(7)               The ascus will have 4 or eight ascospores, which are released when the ascus ruptures.

(8)               The ascospores germinate into + or- hyphae starting the cycle over again.

E.                  The Deuteromycota--the imperfect fungi.

1.                  The Deuteromycota is a “dumping ground” for those Fungi for which a sexual cycle is unknown.

2.                  This clade is not monophyletic and will one day “disappear” as sexual cycles are induced, and genetic analysis determines to which of the other clades they actually belong.

3.                  Many imperfect fungi produce conidospores and are probably Ascomycota--Penicillium and Aspergilliusare examples.

4.                  The Deuteromycota includes many beneficial and dangerous members: Penicillium is responsible for the drug penicillin and Roquefort and blue cheese, Aspergillums species that grow on peanuts are responsible for aflatoxins.

I.                    Characteristics of the Plantae clade (Kingdom).

A.                 Plant cells have a cell wall composed primarily of cellulose.

B.                 Plants store energy as starch (amylose and amylopectin).

C.                 Most plants are multicellular and show well developed tissues.

D.                 Plant plastids contain the photosynthetic pigments chlorophyll-a and b, xanthophylls, beta-carotene, and other characteristic carotenoids.

II.                 Plants are classified according to their structure and life cycles.

A.                 Plants, and to a lesser degree some algae and fungi practice life cycles that involve an "alternation of generations.”

1.                  Alternation of generations is a reference to a life cycle in which plants that are diploid (2n, have two sets of chromosomes), give rise to plants that are haploid (1n, have one set of chromosomes), which in turn give rise to plants that are diploid once again, in a sexual process.

2.                  Alternation of generations for non-Chlorophyta plants is described below.

a)                  We will begin with the sporophyte plant.

(1)               The sporophyte is a diploid plant.

(2)               As the name implies it will produce spores, which are haploid.

b)                  The sporophyte plant develops sporangia, and specific cells within the sporangia undergo meiosis, yielding haploid spores.

c)                  The spores are released from the sporangia, and are disseminated by wind or water.

d)                  Spores germinate into multicellular haploid plants called gametophytes.

(1)               Gametophytes are haploid plants that produce gametes.

(2)               The gametophyte plant produces gametes within structures called gametangia.

(a)                A gametangium that produces female gametes is called an archegonium.

(b)               A gametangium that produces male gametes is called an antheridium.

(3)               Sperm are released from the antheridium and must swim (in primitive plants), or are carried by wind or pollinators (in advanced plants) to the ova.

(4)               Homosporous plants produce spores of one “type.”

(a)                Spores germinate into a gametophyte.

(b)               The gametophyte plant bears both antheridia and archegonia.

(5)               Heterosporous plants produce spores of two “types”--microspores and megaspores.

(a)                Microspores germinate into male gametophytes (microgametophyte) that bear only antheridia (and sperm).

(b)               Megaspores germinate into female gametophytes (megagametophyte) that bear only archegonia (and ova).

e)                  A sperm fertilizes an ovum yielding a diploid zygote.

f)                    The diploid zygote mitotically divides into a new diploid sporophyte.

3.                  A few additional comments about alternation of generations.

a)                  Plants alternate between a diploid, or sporophyte, generation and a haploid, or gametophyte generation, hence the term “alternation of generations.”

b)                  The gametophyte generation dominates in primitive plants, and the sporophyte generation dominates in more advanced plants.

c)                  It is possible for the sporophyte to grow directly on a gametophyte, in which case it is called a parasitic sporophyte.

d)                  It is possible for a gametophyte to grow within a sporophyte, in which case it is called a parasitic gametophyte.

B.                 Chlorophyta and other primitive plants (Bryophyta) have all requirements met from a single environment.

1.                  CO₂, H₂O, dissolved minerals from their aquatic surroundings.

2.                  Light from sun, obviously more intense at surface.

3.                  Support from the natural buoyancy of tissues in an aquatic environment.

C.                 Terrestrial plants have more complex problems, as they must obtain necessities from two environments.

1.                  CO₂, and light from the atmosphere.

2.                  H₂O, dissolved nutrients from the soil.

3.                  Adaptations to this dual environment.

a)                  Shoot system.

(1)               Leaves to create high surface to volume ratio for absorption of light and CO2.

(2)               Support tissues for leaves, stems, and branches, flowers, etc., to offset gravity.

(3)               Waterproofing (suberin, cutin, and waxes = cuticle) of entire shoot system.

(4)               Stomata on undersides of leaves to permit uptake of CO₂, with as little H₂O loss as possible, regulated by guard cells.

(5)               Vascular system (xylem and phloem) for distribution of water, nutrients, and photosynthetic products, within and between the root and shoot system.

(6)               Defense mechanisms to inhibit predation by terrestrial herbivores, including spines, distasteful/toxic chemicals.

b)                  Root system

(1)               Root hairs and numerous root branches to form a high surface to volume ratio for efficient uptake of H₂O and minerals, and to anchor plant in soil.

(2)               Vascular system (see above).

D.                 What are the vascular tissues and how do they function?

1.                  Xylem=composed of cells that are originally alive, but as the secondary wall is lignified, cell dies, as dies perforations (pits) are created in cell wall (ends and sides) by lysosomes.

a)                  Types of xylem cells:

(1)               Tracheids.

(a)                Tapered at either end, pits on ends and sides, capillary action reduced, compared to vessel elements.

(b)               Found in more primitive vascular plants.

(2)               Vessel elements.

(a)                Pits on sides, but open at either end, vessels stacked on another to form long tubules.

(b)               Structure more conducive to capillary action.

(c)                Found in more advanced vascular plants.

(d)               There are numerous types of vessels, many with interesting spiral lignifications in secondary wall.

(3)               Fibers--supportive, do not conduct liquid.

b)                  Transports water and dissolved minerals from roots to shoot.

c)                  Functions via transpiration, which is dependent on three related forces.

(1)               Root pressure.

(a)                Water diffuses into the roots due to the osmotic pressure, and capillary action of cellulose fibers of cell walls.

(b)               Apoplastic absorption is diffusion of water between cells.

(c)                Symplastic absorption is diffusion of water from cell to cell through cell membranes.

(d)               The casparian strip, a ribbon of suberin/lignin, creates a water impermeable barrier around the cells of endodermis.

(e)                It prevents apoplastic diffusion of water into the vascular cylinder of roots.

(f)                 Forces water to diffuse through the endodermal cells (cell membrane), affording at least some control of what enters the xylem.

(g)                Xylems, remember, are dead cells with no cell membranes, once substance in xylem will be carried throughout plant.

(h)                Root pressure is an osmotic pressure and will force water some distance up the stem.

(i)                  Is responsible for guttation, where root pressure so great, water forced out of leaf veins forming droplets along margin.

(2)               Capillary pressure generated by the xylem capillaries of vessel elements and tracheids.

(3)               Evaporative pressure or transpirational pressure.

(a)                Root pressure and capillary pressure alone not enough to move water through stems of most trees.

(b)               As water lost from stomata creates a negative pressure at top of tree/leaves, and water moves up to fill that vacuum.

(c)                The cohesiveness of water is important to this process, as water molecules pull molecules up as evaporate out of leaf.

(d)               The water column of the vessels and tracheids must remain intact for transpiration to continue, if water column broken, that set of xylem no longer transpirational/functional.

(e)                Ninety percent of the water absorbed by the roots lost via transpiration.

2.                  Phloem=living cells that transport sugars from their sources (leaves) to various "sinks" (roots, fruit, meristems, and other dividing tissues).

a)                  Sieve tubes.

(1)               Actual vascular cells.

(2)               No nucleus, organelles, but cell membrane intact, necessary for active transport.

(3)               Large holes in ends of sieve tubes=sieve plates, allow for bulk flow of sap, created by lysosomes.

b)                  Companion cells.

(1)               Not vascular.

(2)               Nucleated, connect to sieve tubes via plasmodesmata.

(3)               Maintain membranes of sieve tubes and regulate translocation.

c)                  Translocation= movement of sugars within phloem.

(1)               At sugar sources sucrose "loaded" into phloem via active transport.

(2)               Sucrose follows concentration gradient to "sinks"; active transport helps to move along.

(3)               Water also follows concentration creating a "bulk flow" of sap 10,000x the speed of simple diffusion alone.

(4)               At "sinks" sucrose actively removed from phloem, and split into simple sugars, maintaining concentration gradients.

(5)               The mechanism of translocation as described above is the Munch Hypothesis.

(6)               If you steam heat phloem, it "kills" the membranes and translocation stops.

(7)               Aphids use tube-like mouth (styled) to penetrate phloem, and feed on sugars.  If you cut the styled from the aphid, leaving the stylet embedded in the phloem, phloem sap exudes from the stylet.

(8)               This requires a positive pressure.

(9)               Led to bulk flow hypothesis.

(10)           Phloem loading stops after dark, as no new sugars being produced.

III.               Plant clades (Divisions) and relationships are described below.

A.                 The Chlorophyta form a monophyletic clade with the plants.

1.                  The Chlorophyta and plants store starch.

2.                  The Chlorophyta and plant plastids contain the same photosynthetic pigments: chlorophyll-a and b, xanthophylls, beta-carotene, and other characteristic carotenoids.

3.                  The Chlorophyta and plants have cellulose cell walls.

4.                  Includes unicellular (Chlamydomonas), colonial (Volvox) and multicellular (Ulva, Ulothrix) genera.

5.                  The Chlorophyta exhibits a variety of life cycles, although at least one species demonstrates an extreme form of anisogamy called oogamy--flagellated “sperm” and nonmotile large “ovum” (same as in plants).

6.                  The Chlorophyta evolved approximately 1.6 ba in the Lower Proterozoic era of the Precambrian time period, probably sharing a common ancestry with the Rhodophyta.

7.                  All other plant clades trace their ancestry to the Chlorophyta, probably a clade called the Stoneworts.

a)                  Stoneworts show numerous genetic, physiological, and morphological homologies.

b)                  They are a classic ambiguous group, that shows both ancestral and derived characteristics making their classification difficult.

B.                 There are at least three important non-tracheophyte (avascular) clades (Divisions), sometimes referred to as the “Bryophytes”.

1.                  The "Bryophytes" have the following characteristics.

a)                  Are avascular, i.e. they lack xylem and phloem, so water and sugars must diffuse from call to cell.

b)                  They are gametophyte dominant, which means that in the plant life cycle the gametophyte is the longer lived and larger plant.

c)                  They require water for fertilization.

d)                  They lack true roots, leaves, and stems.

e)                  They have structures called rhizoids, instead of roots.

f)                    The sporophyte grows from the archegonium of the gametophyte and is describe as a “parasitic” sporophyte.

g)                  Generally prefer moist areas with shade.

2.                  The “Bryophytes” include the clades (Divisions) Bryophyta, Hepaticophyta, and Antherocerophyta.

a)                  The Divisions have morphological differences in both the gametophyte and sporophyte--these differences will be considered in detail in the laboratory.

b)                  Members of the Division Bryophyta are known as the mosses.

(1)               The gametophyte is “bushy” in appearance.

(2)               The archegonia and antheridia are born at the tips of the thalli.

(3)               Moss life cycle.

(a)                The moss you typically see is the haploid gametophyte.

(b)               Gametes are produced at the tip of the plants.

(c)                Sperm are released and must swim to the ova and fertilize them within the tip of the gametophyte.

(d)               The diploid zygote grows into a diploid sporophyte out of the tip of the gametophyte (parasitic sporophyte).

(e)                Haploid spores are produced within the sporophyte and disseminated.

(f)                 The haploid spores germinate into another haploid gametophyte.

(g)                Mosses require water for fertilization (for the sperm to swim), which limits their distribution to moist habitats.

c)                  Members of the Division Hepaticophyta are known as the liverworts.

(1)               The gametophytes grow in liver shaped, ground hugging thalli.

(2)               The gametophytes grow distinctive gametangiophores, which in turn produce gametangia and gametes.

(a)                The antheridiophore is disc like and antheridia are on the upper surface.

(b)               The archegoniophore is “palm tree” like, and archegonia are born on the lower surface.

(c)                The life cycle otherwise is much like the moss, described above.

(3)               The liverworts reproduce asexually by means of gemmae.

(a)                Gemmae are disc like masses of haploid gametophyte cells that are borne in cup like structures called gemmae cups.

(b)               The gemmae are washed from the cups by water, and germinated into haploid gametophytes.

d)                  Members of the Division Antherocerophyta are the hornworts.

(1)               The gametophyte is liverwort like in appearance.

(2)               They do not produce gametangiophores.

(3)               The sporophytes are extremely long and horn like, and grow at their base, rather than at the tip (as do Bryophyta and tracheophytes (described below)).

(4)               The life cycle otherwise is much like the moss, described above.

3.                  Even though the bryophytes are morphologically, and embryologically less complex than the tracheophytes (vascular plants), they do not appear to be ancestral to the tracheophytes.

a)                  Bryophytes and tracheophytes probably evolved independently from Chlorophytan ancestors.

b)                  The Bryophytes do not appear in the fossil record until approximately 385 ma, in the Devonian period of the Paleozoic era, much later than the first tracheophytes (approximately 430 ma in the Silurian period of the Paleozoic era).

4.                  Liverworts probably are ancestral group that gave rise to Hornworts which gave rise to Mosses.

IV.              I would first like to consider the non-seed producing tracheophyte (vascular) clades (Divisions)--which are summarily referred to as “embryophytes.”

A.                 Characteristics of the tracheophytes.

1.                  They are sporophyte dominant.

2.                  All members have vascular tissues.

B.                 The ancestral tracheophyte clade is the Rhyniophyta.

1.                  They evolved approximately 430 ma in the Silurian period of the Paleozoic era, and are now extinct.

2.                  They lacked true roots, and leaves, although they were clearly vascular, and sporophytes.

a)                  Roots have vascular tissues in the center of the root, in a so-called vascular cylinder.

(1)               Rhizoids are root like but avascular.

(2)               Tubers are a storage root (potato).

(3)               A taproot is a large central root (carrot).

(4)               Fibrous roots are as described, and lack a taproot.

b)                  Stems have vascular tissues in scattered bundles, peripheral bundles, or rings.

(1)               Stolons are horizontal stems that may grow along the ground (Bermuda grass).

(2)               Rhizomes are underground stems, often used for storage (ferns, ginseng)--roots branch from rhizomes.

c)                  Leaves typically have linear bundles of vascular tissues, or central bundles, but always above ground--leaf morphologies will be addressed in the laboratory.

3.                  The Rhyniophyta life cycle.

a)                  The sporophyte bore capsule-like sporangia, within which, meiosis led to production of spores.

b)                  The gametophytes are not known from the fossil record.

C.                 The (Division) Psilophyta, known as the "slender plants,” or “whisk ferns” are a modern plant group that morphologically resembles the Rhyniophyta.

1.                  They lack true leaves.

2.                  They lack true roots, although do have a rhizome.

3.                  Were thought to be living representatives of the Rhyniophyta, but the fossil record (a 300 million year gap) and DNA analysis suggest otherwise.

4.                  Life cycle.

a)                  Bulb like sporangia form on the stem of the diploid sporophyte.

b)                  Haploid spores are produced within the sporangia.

c)                  Spores are released and germinate into haploid gametophytes.

d)                  Gametophytes produce sperm within antheridia and ova within archegonia.

e)                  Sperm from one plant swim to another and fertilize an ovum within an archegonium.

f)                    The diploid zygote grows into a diploid sporophyte, destroying the gametophyte in the process.

g)                  Example: Psilotum.

D.                 The (Division) Lycophyta (the club mosses) evolved from the Rhyniophyta approximately 400 ma in the lower Devonian period of the Paleozoic era--Lycophytans have the following characteristics.

1.                  Lycophytans have true leaves and roots (although small).

2.                  Though limited to only four tropical genera today, they were once the dominant flora in the fossil record, including many arboreal species.

3.                  Life cycle.

a)                  The diploid sporophyte produces structures called strobila (cones).

b)                  The strobila are modified buds.

c)                  The sections, or scales of the strobilus are modified leaves, and are called sporophylls.

d)                  At the base of the sporophylls sporangia form.

e)                  Within the sporangia haploid spores are produced--most species are heterosporous.

(1)               Microsporangia are released and germinate into haploid microgametophytes.

(2)               Megasporangia are released and germinate into haploid megagametophytes.

f)                    Microgametophytes produce sperm within antheridia and megagametophytes produce ova within archegonia.

g)                  Sperm swim to the ova and fertilize them within the archegonia.

h)                  The diploid zygote divides and forms a new diploid sporophyte destroying the gametophyte in the process.

i)                    Example: Lycopodium.

E.                  The (Division) Sphenophyta (the horsetails) evolved from the Rhyniophyta approximately 380 ma in the middle Devonian period of the Paleozoic era--Sphenophytans have the following characteristics.

1.                  True roots and leaves.

2.                  Leaves grow in whorls at the nodes of the stems.

3.                  Stems grow at the base of each node.

4.                  Stems are hollow and cell walls contain silica--was used as a scrub brush by Native Americans and settlers.

5.                  Comments on evolution.

a)                  They replaced the Lycophyta as the dominant plant in the fossil record, showing tremendous diversity (with numerous arboreal species).

b)                  The Sphenophyta thrived well into the Carboniferous period of the Paleozoic era, and is a major component of ancient coal forming forests (along with the ferns.

c)                  Life cycle.

(1)               The diploid sporophyte produces structures called strobila (cones).

(2)               The strobila are modified buds.

(3)               The sections, or scales of the strobilus are modified leaves, and are called sporophylls.

(4)               At the base of the sporophylls sporangia form.

(5)               Within the sporangia haploid spores are produced.

(6)               Spores are released and germinate into haploid gametophytes.

(7)               Sperm of one gametophyte swim to the ova of another gametophyte and fertilize them within the archegonia.

(8)               The diploid zygote divides and forms a new diploid sporophyte destroying the gametophyte in the process.

d)                  Relatively few species today, but not an uncommon plant (just look outside my office).

e)                  Example: Equisetum.

F.                  The (Division) Pterophyta (the ferns, although literally = the wing leafed plants) evolved from the Rhyniophyta approximately 370 ma in the late Devonian period of the Paleozoic era--Pterophytans have the following characteristics.

1.                  The ferns exhibit structural complexity although they have a primitive life cycle.

2.                  Ferns have true leaves, and a rhizome that bears small, but true, roots.

3.                  Ferns have larger, and more complex leaves, called fronds, than Lycophyta or Sphenophyta.

a)                  The fronds uncoil as they grow forming “fiddleheads.”

b)                  The parts of the frond are the petiole, blade, and leaflets.

4.                  Though structurally complex, fern stems lack cambium.

5.                  Pterophyta also thrived into the Carboniferous period of the Paleozoic era, and are also major contributors to our coal deposits.

6.                  Ferns are still numerous, with about 260 genera, in the world, although generally limited to moist areas.

7.                  The fern life cycle is described below.

a)                  The fern is the diploid sporophyte.

b)                  On the bottom of the frond leaflets, structures called sori develop.

c)                  Sori are clusters of sporangia, within which, haploid spores develop--both homosporous and heterosporous species exist.

d)                  Spores are disseminated and develop into haploid gametophytes.

e)                  Male gametophytes produce flagellated sperm, which swim to ova on female gametophytes and fertilize them, producing diploid zygotes.

f)                    The zygotes grow into new diploid ferns.

8.                  The fern life cycle is considered primitive for the following reasons.

a)                  Water is necessary for fertilization.

b)                  The gametophyte is free living.

c)                  Plants that require water for fertilization do not produce seeds, so ferns are not seed producing plants.

V.                 The remaining plant clades (Divisions) are seed producing plants, called spermophytes.

A.                 Since we are discussing seed producing plants it is important to understand the parts of a seed.

1.                  Seed coats are the external coatings of a seed and are protective.

a)                  They develop from structures called ovules, one ovule produces one seed.

b)                  The seed coats are diploid.

2.                  The embryo (embryonic plant) develops from the zygote--the embryo is the diploid sporophyte of the next generation.

3.                  Endosperm is nutritive material that supplies food to the growing embryo until it can begin photosynthesizing for itself--as we will see below, the endosperm will be either haploid or triploid.

B.                 The evolutionary importance of the seed is related to the seed producing life cycles, and cannot be overstated (much of this will not make sense until we have discussed spermophyte life cycles).

1.                  Seed producing plants produce pollen grains, and pollen grains produce sperm nuclei--water is not required for fertilization by seed producing plants.

2.                  As a result, seed producing plants were able to invade drier habitats as never before--water was still required for the activities of life, but not required for sexual reproduction.

3.                  Seeds give the embryonic sporophyte a “head start” by means of the endosperm--this lead to greater reproductive success than spores and free-living gametophytes.

4.                  Offspring were disseminated as never before.

a)                  No longer dependent on water or wind, seeds were collected and distributed over wide areas by animals that collected and ate them for their nutritive value.

b)                  This is taken to another level by the flowering plants, which may have edible fruits, which also invite animal distribution.

5.                  Spermophytes dominate the fossil record soon after their appearance and are still the dominant flora today (in the form of the Anthophyta).

C.                 The following clades (Divisions) are described as “gymnosperms,” forming a paraphyletic group (the Gnetophyta are probably ancestral to the Anthophyta).

1.                  The (Division) Coniferophyta (the cone bearers) evolved from the Pterophyta approximately 320 ma in the Mississippian period, a subdivision of the Carboniferous period of the Paleozoic era--Conifers have the following characteristics.

a)                  Most conifers have needle-like leaves and are evergreens.

b)                  Conifers produce seeds that develop within cones.

c)                  Cones are modified buds; the “scales” of a cone are modified leaves.

d)                  The cones are reproductive organs of a conifer.

e)                  The life cycle includes parasitic gametophytes.

f)                    Examples--pines, firs, junipers, etc.

g)                  They and all gymnosperms have cambium and exhibit secondary growth.

h)                  All gymnosperms but the Gnetophyta have only tracheids in the xylem.

i)                    The conifer life cycle does not require water for fertilization and is described below.

(1)               The conifer tree is the diploid sporophyte plant.

(2)               The scales of the cone contain sporangia.

(3)               Male cones.

(a)                Each scale of the cone develops a sporangium within which numerous haploid spores develop--they are called microspores.

(b)               The spores are not disseminated, but divide to form a binucleate pollen grain--this is the microgametophyte (the spore becomes the gametophyte when it starts dividing).

(c)                The mature pollen grains (microgametophytes) are disseminated and captured by the wind and may stick in the sap of a green female cone (see below).

(4)               Female cones.

(a)                At the base of each scale, sporangia develop within structures called ovules--there are typically two ovules per scale.

(b)               A haploid megaspore develops within each ovule.

(c)                The megaspore is not disseminated but develops into a small megagametophyte within the ovule.

(d)               The megagametophyte produces an ovum.

(e)                Pollen grains are captured in the sap of the green developing female cone.

(5)               The pollen grain is pulled into the space between the scales of the cone as the sap dries.

(6)               One of the nuclei of the pollen grain is a tube nucleus; the other is a generative nucleus.

(a)                The tube nucleus controls growth of the pollen grain, as it extends a “tube” towards the ovule and ovum.

(b)               The generative nucleus divides to form two sperm nuclei in most species.

(c)                When the pollen tube fuses with the gametophyte, one of the sperm nuclei fuses with the ovum nucleus to form a zygote, the other disintegrates.

(7)               The zygote develops into the embryo of the seed.

(8)               The rest of the gametophyte develops into the endosperm of the seed.

(9)               The surrounding ovule develops into seed coats.

(10)           The seeds are disseminated when the cone desiccates and opens up.

(11)           Wind, water, and animals disseminate seeds.

(12)           The seeds grow into a new sporophyte.

2.                  The importance of pollen grains is that they do not require water for fertilization.

3.                  This allowed conifers, and other gymnosperms, to invade drier habitats.

4.                  The process is usually a two-season process.

5.                  The (Division) Cycadophyta (the sago palms) evolved from primitive Conifers approximately 240 ma in the Triassic period of the Mesozoic era--Cycads have the following characteristics.

a)                  They have palm like leaves, but are not true palms (palms are flowering plants).

b)                  They are dioecious (separate sexes, monecious means both male and female reproductive organs on same plant).

c)                  Male plants grow large cones at the top of the plant that produce pollen.

d)                  Female plants generally bear naked seeds (not protected by cones or fruit) on a single stem like axis.

6.                  The Ginkgophyta (maiden hair trees) evolved from primitive Conifers approximately 220 ma in the Triassic period of the Mesozoic era--Ginkgoes have the following characteristics.

a)                  Only one extant species, Ginkgo biloba, rediscovered in China.

b)                  Fan shaped leaves, with parallel venation.

c)                  Ginkgoes are dioecious.

d)                  Male trees bear microstrobila and pollen; the female bears "naked" seeds with a pungent odor.

e)                  Are also deciduous--drop leaves in fall, regrow in spring.

7.                  The Gnetophyta evolved from primitive Cycads approximately 220 ma in the Triassic period of the Mesozoic era--Gnetophytans have the following characteristics.

a)                  They are an enigmatic group, probably ancestral to the Anthophyta (flowering plants).

(1)               Like Anthophytes they have vessel elements, although they may have evolved independently.

(2)               At least some practice double fertilization--previously thought unique to flowering plants.

b)                  Pollen may be born on microsporophylls that are flower like (staminate flowers).

c)                  Ovules and seeds are borne singly and naked.

d)                  Example: Ephedra.

D.                 The (Division) Anthophyta (the flowering plants, formerly called the angiosperms) probably evolved from Gnetophyta approximately 150 ma in the Jurassic period of the Mesozoic era--flowering plants have the following characteristics.

1.                  The division is characterized by the presence of a flower, and seeds that develop within a fruit.

2.                  Angiosperms carry out “double-fertilization.”

3.                  Flowering plants produce pollen, and so, do not require water for fertilization.

4.                  The anatomy of the flower.

a)                  The receptacle is the part of the stem supporting the flower.

(1)               If the pistil (carpel) is above the receptacle the flower has a superior ovary.

(2)               If the pistil (carpel) is embedded in the receptacle the flower has an inferior ovary.

b)                  The sepals are typically green, and surround the flower bud--the sepals collectively are called the calyx.

c)                  The petals are normally pigmented to attract pollinators--the petals collectively are called the corolla.

d)                  The pistil (or carpel) is the female reproductive organ, and is composed of the stigma, style and ovary.

(1)               Within the ovary is one to many ovules.

(a)                Each ovule contains a single female gametophyte (a parasitic gametophyte), which will contain a single ovum.

(b)               A single ovule yields a single seed.

(2)               The ovary develops into a fruit.

(3)               Carpels are sometimes fused, making it difficult to tell how many carpels there are (which is important in classification).

e)                  The stamen is the male reproductive organ, and is composed of the anther and filament--stamens may be attached to the pistil or other flower parts.

5.                  Angiosperms may be either monecious or dioecious.

a)                  Monecious--one plant has both sexes.

(1)               May be separate male flowers (with only stamens), and female flowers (with only pistils).

(2)               May have individual flowers, which contain both sexes.

b)                  Dioecious--are separate male and female plants.

(1)               Male plants have only male flowers.

(2)               Female plants have only female flowers.

6.                  The life cycle of an angiosperm is described below.

a)                  The flowing plant is the diploid sporophyte plant.

b)                  The flower has the male and female reproductive organs.

c)                  Pollen grains develop within the anthers of the stamens.

(1)               Within the anther, sporangia develop, and produce haploid spores called microspores.

(2)               The microspore nuclei divide yielding a binucleate pollen grain, which is now a microgametophyte (the spore becomes the gametophyte when it starts dividing).

(3)               The anthers split open exposing the pollen grains.

(a)                Some flowering plants are wind pollinators.

(b)               Most flowering plants require a pollinator (some animal) to transport pollen grains to the stigma of another flower.

d)                  Meanwhile, within the carpel/pistil...

(1)               Ovules develop within the ovary of the carpel.

(2)               Within the ovules a haploid megaspore forms, and grows into an eight-celled megagametophyte within the ovary.

(3)               One of the cells is an ovum; two cells are called polar bodies.

e)                  Pollen is delivered to the stigma of the carpel.

f)                    One of the nuclei directs growth of an extension of the pollen grain, called a pollen tube, through the style to the ovary, and eventually to an ovule.

g)                  As the pollen tube extends, the other nucleus, called a generative nucleus, divides to form two sperm nuclei.

h)                  When the pollen tube gets to the megagametophyte the following occurs:

(1)               One sperm nucleus fuses with the ovum to form a diploid zygote--the zygote will grow to form the embryo of the seed.

(2)               The other sperm nucleus will fuse with two nuclei of the megagametophyte called polar nuclei, to form a 3n cell (the two polar nuclei and sperm are all haploid = 3n)--this triploid cell will divide to form the endosperm of the seed.

(3)               The ovule will form the seed coats of the seed.

i)                    The seeds of a flowering plant have a triploid endosperm; this is unique to flowering plants.

j)                    The seeds are disseminated and grow into new sporophytes.

7.                  Some common terms associated with flowers are discussed below.

a)                  Perfect flowers have both male and female reproductive organs.

b)                  Imperfect flowers do not.

c)                  Complete flowers are perfect flowers with petals, and sepals.

d)                  Incomplete flowers lack one or more of these.

e)                  Regular flowers have radial symmetry.

f)                    Irregular flowers have bilateral symmetry.

8.                  Angiosperms are unique in another way --a fruit protects the seeds.

a)                  A fruit is any kind of ripened ovary, within which, are seeds.

b)                  There are 3 major layers to the ovary.

(1)               The pericarp--the outer layer of cells.

(2)               The mesocarp--the middle layer of cells.

(3)               The endocarp--the inner layer of cells (adjacent to the ovules).

c)                  Fruits are categorized in many ways.

(1)               Fleshy fruits

(a)                One or more of the ovary layers are fleshy; examples = grape, banana, watermelon, orange.

(b)               Drupes are a type of fleshy fruit in which the endocarp forms a hard "pit" or "stone", e.g. peaches, nectarines, etc.

(2)               Dry fruits--mature fruit lacks fleshy tissue.

(a)                Dehiscent fruits--dry fruits that split along a seam to distribute seeds such as bean and pea pods.

(b)               Indehiscent fruits--dry fruits that do not split on a seam such as corn, wheat, and other grains.

(3)               Simple fruits form from a single carpel or several united carpels--e.g. Cherry, orange, tomato, etc.

(4)               Aggregate fruits form from several separate carpels of a single flower, forming separate fruitlets--e.g. Raspberry, blackberry, etc.

(5)               Multiple fruits form from a cluster of separate flowers (inflorescence) that fuse into a single fruit as they develop--e.g. Pineapple and fig.

(6)               Accessory fruits--flower parts other than the ovary help form the fruit (receptacle, calyx, etc.) such as strawberries, apples, pears, bananas, etc.

9.                  There are two clades (Classes) of flowering plants that are generally recognized.

a)                  Before discussing these clades, we need to reconsider Anthophyte seed structure in more detail, as well as the seedlings that grow from them.

(1)               As mentioned earlier the seed is composed of a seed coat, endosperm, and embryo.

(a)                The seed coat is protective.

(b)               The endosperm stores nutritive products--starch, oils, protein, minerals, vitamins, etc to be absorbed by the developing seedling.

(c)                The embryo, which grows into a seedling as it absorbs nutrients from the endosperm until it can begin photosynthesizing, and absorbing soil nutrients on its own.

(2)               The embryo of the plant has the following parts.

(a)                Plumule--grows into the leaves of the embryonic plant.

(b)               Radicle--will be the tip of the embryonic root.

(c)                Cotyledon--so-called “seed leaf,” acts as an interface between the embryo and the endosperm.

(i)                  Some seeds have a single cotyledon, called a scutellum, and are considered “monocots”-- corn seeds are an example.

(ii)                Some seeds have two cotyledons, and are called “dicots”-- bean seeds are an example.

(3)               In some seeds (more typically monocots) the endosperm makes up the bulk of the seed, and the cotyledon absorbs the endosperm within the seed, and does so gradually as the embryo germinates into a seedling.

(a)                In a corn seed the “disc” with the point on the end is the embryo with its cotyledon.

(b)               The “mush” is the endosperm.

(4)               In other seeds (more typically dicots) the cotyledons absorb nutrients from the endosperm before the seed germinates into a seedling, such that the bulk of the seed is composed of the cotyledons, swollen with nutrients absorbed from the endosperm (beans, peas, peanuts).

(a)                The “halves” of the seed are the cotyledons.

(b)               The embryo is clearly visible as a small plant.

(c)                Endosperm is absent.

(5)               When the embryo germinates terms are used relative to the cotyledon position.

(a)                The epicotyl is the part of the seedling above the site where the cotyledon(s) attach to the seedling--some of the epicotyl may be below ground.

(b)               The hypocotyl is the part of the seedling below the site where the cotyledon(s) attach to the seedling--some of the hypocotyl may be above ground.

(6)               The nature of the seed is used for classifying flowering plants.

b)                  Characteristics of the Class Monocotyledonae, also called the monocots.

(1)               The seed has a single cotyledon.

(2)               Vascular bundles in herbaceous plants scattered randomly throughout stem.

(3)               Leaves show parallel venation.

(4)               Flower parts (sepals, carpels, petals, etc.) usually in 3's, or multiples of 3.

(5)               Roots usually fibrous (scattered).

c)                  Characteristics of the Dicotyledonae, also called the dicots

(1)               Two cotyledons in a seed (like beans, peanuts, etc.).

(2)               Vascular bundles in herbaceous stems arranged in a circle around the periphery of stem.

(3)               Leaves show netted venation.

(4)               Flower parts usually in 4's, 5's or multiples of these.

(5)               Roots usually show a taproot (a large central), with smaller branches.

(6)               Examples--beans, peas, peanuts, apples, pears, peaches, etc.

VI.              Plant tissues.

A.                 Apical meristem= a mitotic, embryonic tissue found at stem and root tips, gives rise to other meristems mentioned below, and is responsible for primary growth (increase in length) of a plant.

B.                 Ground meristem= produced by apical meristem and continues to divide and gives rise to the "ground tissues", e.g., parenchyma, collenchyma, schlerenchyma, some cambium.

C.                 Protoderm=produced by apical meristem and gives rise to epidermis, and cork cambium in some plants.

D.                 Provascular tissue= produced by apical meristem and gives rise to xylem, phloem, and vascular cambium.

E.                  Parenchyma=large thin walled cells of stem and root, found in both cortex and pith, have intracellular spaces between cell walls, storage cells for starch or water, are living and can divide when stimulated to do so.

F.                  Collenchyma= smaller than parenchyma, cell wall of uneven thickness, flexibly supportive because of the cellulose cell wall, have potential to divide, if intracellular spaces are small.

G.                 Sclerenchyma= cells with lignified cell walls, rigid support, found associated with vascular bundles, woody xylem, and fruit.

1.                  Fibers=support fibers of vascular tissue, non-conductive, dead.

2.                  Sclerids=irregular shaped cells, form grit in some fruits (pears), and shells of some fruits (peach pit, walnuts, etc.).

H.                 Cambium=mitotic, accounts for secondary growth (increase in girth) of plants that have it.

I.                    Vascular (fascicular) cambium= produces both xylem and phloem, as well as bundle fibers, and in woody plants woody parenchyma.

J.                   Interfasciular cambium=found between vascular bundles of herbaceous plants, producing parenchyma.

K.                Cork cambium=produces cork of woody trees and probably some collenchyma/parenchyma, is external to phloem.

L.                  Pericycle/lateral meristem= gives rise to lateral branches in root.

M.               Periderm=suberized cells of bark (cork), some consider this a type of collenchyma.

VII.            Plant hormones--means of chemical communication within plant, different parts of plant may react differently to same hormone.

A.                 Auxins= Indole Acetic Acid (IAA)

1.                  Review Charles and Francis Darwin's discovery that the tip of coleoptiles responds to light, and Went's discovery of chemical nature of auxin.

2.                  Effects:

a)                  Cell elongation.

b)                  Apical dominance.

c)                  Abscission suppression.

d)                  Fruit maturation.

e)                  Xylem differentiation.

f)                    Stimulates cambium, secondary growth.

g)                  Geotropism.

h)                  Synthetic auxins used as herbicides, include Agent Orange, plants "grow themselves to death", does not affect monocot grasses.

B.                 Giberellins= Giberellic acid most common (GA).

1.                  Originally discovered as a fungus product, found in young leaves of plants.

2.                  Effects:

a)                  In some plants stimulates maturation, in other plants stimulates reversion to juvenile status.

b)                  Releases some buds and seeds from dormancy, results in growth (dwarf plants lack giberellins).

c)                  Related to flowering in some plants as concentrations change in relation to day length.

d)                  Causes stem elongation.

e)                  Stimulates pollen tube growth in angiosperm reproduction.

C.                 Cytokinins

1.                  Chemically are purines, related to adenine, first found in roots, seeds.

2.                  Effects:

a)                  Cause cell division, especially in combination with auxins and sucrose.

b)                  Stimulate bud growth.

c)                  Stimulate fruit and embryo development.

d)                  Prevents leaf senescence.

e)                  Mimics effects of phytochrome.

D.                 Abscisic acid (ABA)

1.                  General growth inhibitor.

2.                  Induces dormancy in buds and leaves (winter).

3.                  Closure of stomata.

4.                  Resistance to stress.

5.                  Probably not involved in abscission.

E.                  Ethylene= a gaseous hormone,

1.                  Plays a role in fruit ripening.

2.                  Fruit abscission.

3.                  Stimulates own production in many fruits.

4.                  Initiation of root hairs.

F.                  Phytochrome=flowering hormone.

1.                  Many plants flower in response to "day length", and are categorized as short-day and long-day plants.

2.                  Was theorized was a light sensitive hormone that regulated flowering, phytochrome thought to be that hormone.

3.                  Two phases.

4.                  Pr absorbs light of 660nm= red phase, is "free", and was once thought to be metabolically inactive.

5.                  Pfr absorbs light of 730nm=far-red phase, binds to membranes and is considered the metabolically active form.

6.                  Pr converted to Pfr in daylight, and at night Pfr reverts back to Pr.

7.                  Was once thought that Pfr concentration critical, that long day plants needed higher concentrations of Pfr to flower, and longer days made that possible.

8.                  Was discovered however that night length is critical, so plants now called short night plants, and long night plants.

9.                  Was hypothesized that Pr concentration critical, and disruption of night cycle prevented adequate concentration of Pr from accumulating.

10.              Now known however that all Pfr converted back to Pr within about three hours.

11.              The role of phytochrome in flowering is obviously confused, may work with giberellins in some as yet undefined way.

G.                 There are numerous interactions between hormones, which vary from plant to plant and tissue to tissue, which still must be defined more clearly--they account for the rhythms we see in plants.

1.                  Circadian rhythms.

2.                  Flowering cycles.

3.                  Seasonal activity, inactivity.

H.                 The plant cell wall contains receptors for hormones, it is not benign, but an active player in cell signaling pathways.

I.                    Eumetazoan (animal) development begins with fertilization.

A.                 Structure of the spermatozoon.

1.                  The head of the spermatozoon contains the sperm nucleus (DNA) and the acrosome (acrosomal vesicle), which contains digestive enzymes that will digest the outer layers of the ovum.

2.                  The neck of the spermatozoon contains mitochondria.

a)                  Was previously thought that these will not penetrate the ovum, and that only maternal mitochondria go to the next generation.

b)                  Recent evidence suggests that male mitochondria do enter the ovum (secondary oocyte), but it is hypothesized that the male mitochondria are marked for destruction, by some as yet undiscovered process.

c)                  Not all male mitochondria are necessarily eliminated, which if true, will alter the accuracy of genetic studies involving mitochondrial genes, especially “clocks.”

3.                  The tail of the spermatozoon is a flagellum that will propel the sperm through water or fluids.

B.                 The structure of the ovum.

1.                  Most ova have an outer layer of glycoprotein termed the zona pellucida in mammals--this layer may contain receptors that will bind spermatozoa.

2.                  Non-mammalian ova may have another layer called the vitelline layer, surrounded by a jelly layer that will bind spermatozoa.

3.                  Internal to the zona pellucida or vitelline layer (if present) is the ovum’s plasma membrane.

4.                  Associated with the plasma membrane will be numerous vesicles called cortical granules.

C.                 Fertilization events.

1.                  The spermatozoa will swim to the ova and bind to receptors in the zona pellucida or vitelline layer.

2.                  The receptors trigger the rupture of the acrosome and the release of its hydrolytic enzymes, as well as the protrusion of a process that will penetrate to the plasma membrane.

3.                  The sperm and ovum plasma membranes will fuse.

4.                  The sperm nucleus will be forced into the ovum, which means fertilization has occurred.

5.                  The ovum must now protect itself from polyfertilization.

a)                  When the sperm and plasma membranes fuse it triggers a cortical reaction in which the cortical granules bind to the plasma membrane, spewing their contents into the space between the plasma membrane and the zona pellucida or vitelline membrane.

b)                  The enzymes from the cortical granules:

(1)               Alter the texture of the zona pellucida so it becomes impenetrable by other spermatozoa.

(2)               Alter the vitelline membrane causing it to expand, pushing the spermatozoa away from the ovum membrane.

c)                  The cortical reaction begins at the site of sperm penetration and spreads around the ovum, as the rupture of one granule affects rupturing of adjacent granules, which in-turn affects still others, and so on.

6.                  The sperm and ovum nuclei fuse, initiating a series of cell divisions (cleavage).

7.                  In mammals, the “ovum” is actually the secondary oocyte, so in addition to the cortical reaction, fertilization causes the ovum to finish meiosis, before the nuclei fuse.

II.                 Cleavage is the early cell division of the zygote yielding cells called blastomeres.

A.                 Cleavage and subsequent cell divisions:

1.                  Reduce cell size to optimum surface area to volume ratio.

2.                  Increase cell number for later differentiation.

B.                 Cleavage follows two general patterns in the animal kingdom.

1.                  Radial cleavage

a)                  Cleavage along alternating meridional (longitudinal) and equatorial (latitudinal) planes.

b)                  Typical of deuterostomate animals, in which the anus is the first intestinal opening to develop.

2.                  Spiral cleavage

a)                  Cleavages are oblique, or not in alternating meridional and equatorial planes.

b)                  Typical of protostomate animals in which the first intestinal opening to form, embryonically, is the mouth.

C.                 Distribution of yolk may be isolecithal (evenly distributed) or telolecithal (yolk concentrated at one end).

1.                  Telolecithal zygotes have a vegetal pole and animal pole.

2.                  Cleavage will be holoblastic (complete) if isolecithal, meroblastic (incomplete) if telolecithal.

III.               Other embryonic stages.

A.                 Cleavage will generate a solid mass of blastomeres called a morula.

B.                 The morula develops into a blastula (or blastodisc), with a central fluid filled cavity called a blastocoele.

C.                 The blastula cells now invaginate and migrate to form the primitive gut and embryonic tissues--the process is gastrulation and the stage produced is the gastrula.

1.                  The gastrula will produce up to three embryonic tissues that will then develop into all adult tissues (epithelium, connective, nervous, and muscle).

a)                  Endoderm--will become the lining of the gut and accessory organs of the digestive cavity.

b)                  Ectoderm--will give rise to skin, hair, nails, nervous tissues.

c)                  Mesoderm--derived from endoderm, found between the tissues described above, gives rise to muscle, bone, connective tissue, coelom develops within mesoderm.

2.                  The primitive gut is called the archenteron or gastrocoele.

3.                  The initial opening (blastopore) by which the blastula invaginates to form the gastrula will develop into an opening for the digestive cavity.

a)                  If that is to be the only opening into the gut then the animal has a closed digestive tract.

b)                  If another opening will later form the animal has an open digestive tract.

(1)               If the blastopore becomes the mouth the animal is a protostomate.

(2)               If the blastopore becomes the anus the animal is a deuterostomate.

D.                 Shortly after gastrulation a coelom may form.

1.                  A coelom is an internal body cavity completely lined by tissue derived from mesoderm, and lacks an opening to the outside.

a)                  A coelom is lined by connective tissue or muscle, both derived from mesoderm.  

b)                  The space between the body organs, in humans, is an example of a coelom, whereas the intestinal tract is not the coelom, because it has openings to the outside of the body. 

c)                  Animals are typically described in one of three ways where body cavities are concerned:

(1)               Acoelomic--without a coelom, or body cavity.

(2)               Pseudocoelomic--a body cavity that is not completely lined by muscle or connective tissue.

(3)               Eucoelomic--a body cavity completely lined by muscle or connective tissue.

2.                  A coelom develops in one of two ways.

a)                  Protostomates are schizocoelomic.

(1)               During gastrulation masses of mesoderm form.

(2)               A cavity forms within these masses of mesoderm forming coeloms.

b)                  Deuterostomates are enterocoelomic.

(1)               During gastrulation the archenteron forms pouches.

(2)               These pinch off creating coelom(s).

IV.              From the three embryonic tissues, cells influence one another in the ongoing process of embryonic development.

A.                 Morphogenic movements

1.                  Some cells become amoeboid and migrate to another location.

2.                  Cells may be adhesive and move in sheets, propelled by motor molecules.

3.                  Moving cells follow a trail of CAM’s = cell adhesion molecules.

B.                 Induction--a process by which the presence of one tissue “induces” changes (differentiation) in an adjacent tissue.

1.                  An inducer may migrate to a new location or the target tissue may migrate to the inducer.

2.                  The inducing tissue releases an inducing chemical that typically leads to a chemical cascade in the target tissue altering gene activity leading to differentiation.

3.                  Example 1: neural tube formation in vertebrates, ectoderm induced by mesoderm.

a)                  Anterior tube = brain

b)                  Post tube = spinal cord.

4.                  Example 2: neural tube will outpocket forming optic vesicles that induce overlying ectoderm to form the lens of the eye.

5.                  Investigation of induction has yielded some interesting results, e.g. if take embryonic flank ectoderm from a frog and explant it to the mouth region of a salamander it will be induced to form a mouth, but will form a frog mouth because of its genetic information.

C.                 Apoptosis--programmed cell death.

1.                  Cells may be destroyed at certain times, and the nutrients used to produce new tissues, e.g. metamorphosis.

2.                  Organs or tissues may have a function that is no longer needed, so cells die, e.g. thymus gland reduction.

3.                  Mitochondria seem to be key to apoptosis--various signals will alter their ability to produce ATP leading to cell death.

D.                 Determination--when the “fate” of a cell is “determined” and cannot be changed.

1.                  At the 32-cell stage of protostomate development, the cells are determinate, i.e. if you remove one of the cells you will have deformity.

2.                  At the 32 cell stage of deuterostomes the cells are indeterminate, if you remove one of the cells, other cells will pick up its role and the embryo will still develop normally.

3.                  What causes determination--determination probably set by mRNA in the ovum cytoplasm that starts a cascade of genetic events as cleavage begins.

E.                  Regeneration--replacement of lost parts by an organism.

1.                  Is embryonic in nature, i.e. cell division, migration, differentiation.

2.                  Examples: planaria, crabs regrow claw, lizard tails, and sponges.

3.                  “Primitive” organisms are better at it.

4.                  Younger organisms are better at it.

5.                  Some organisms may have reserve of stem cells = embryonic cells that do not differentiate.

6.                  Recent cloning experiments show the potential of “dedifferentiating” a differentiated nucleus to produce stem cells that could be used in regenerating therapies.

F.                  Metamorphosis--changing morphology or changing from one form to another.

1.                  Insect

a)                  Complete metamorphosis: egg, larva, pupa, adult.

b)                  Incomplete metamorphosis: egg, nymph(s), adult.

2.                  Marine invertebrates: form 1, form 2, adult (in barnacles: nauplius, cypris, adult).

3.                  Amphibian: larva w/gills, adult w/ lungs.

4.                  Others.

5.                  Metamorphosis typically caused by hormones, e.g. insect molting controlled by ecdysone.

G.                 A comparison of Protostomates and Deuterostomates.

1.                  Protostomates have the following characteristics.

a)                  They develop via spiral cleavage.

b)                  The mouth forms from the blastopore of the gastrula.

c)                  They are schizocoelous.

d)                  Determinate blastomeres.

e)                  Dorsal heart (if present).

f)                    Ventral nerve chord(s).

2.                  Deuterostomates have the following characteristics.

a)                  They develop via radial cleavage.

b)                  The anus forms from the blastopore of the gastrula.

c)                  They are enterocoelous.

d)                  Indeterminate blastomeres.

e)                  Ventral heart.

f)                    Dorsal nerve chord.

V.                 Some terms associated with animal taxonomy.

A.                 Tissue level development.

1.                  Such animals have tissues but lack organs.

2.                  A tissue is a group of cells working for a common function.

3.                  Examples include muscle tissue, nervous tissue, connective tissue, etc.).

B.                 Organ level development.

1.                  Such animals have organs but lack organ systems.

2.                  Organs are composed of tissues working for a common function.

3.                  The heart is an organ composed of connective, cardiac, and epithelial tissues.

C.                 Organ system level development.

1.                  Such animals have organ systems.

2.                  Organ systems are composed of organs working for a common function.

3.                  Eleven organ systems are traditionally recognized, and these will be considered in more detail as we discuss animal evolution.

a)                  Integumentary system (skin).

b)                  Muscular system.

c)                  Skeletal system.

d)                  Nervous system.

e)                  Excretory system (nitrogenous wastes).

f)                    Digestive system.

g)                  Immune system.

h)                  Cardiovascular system.

i)                    Reproductive system.

j)                    Lymph(atic) system.

k)                  Endocrine system (hormones).

D.                 Coelom--discussed above.

E.                  Symmetry--an animal has symmetry if there is a plane by which an animal can be divided to get mirror images.  There are three terms related to symmetry.

1.                  Amorphous (asymmetry)--without symmetry.




 

2.                  Radial symmetry--multiple planes will divide the organism into mirror images.






 

3.                  Bilateral symmetry--only one plane will divide animal into mirror images.






 

F.                  Closed digestive system--the digestive tract is like a bag, in that it has only one opening that serves as both mouth and anus.

G.                 Open digestive system--the digestive system is like a tube, open at both ends, one opening a mouth, the other the anus.

VI.              There are numerous directional/anatomical terms that will be relevant when discussing/dissecting animals, and these are listed below.

A.                 Anatomical position-- “standing” position (palms forward in human).

B.                 Anterior-- (towards the) front.

C.                 Posterior-- (towards the) rear.

D.                 Dorsal-- (towards the) back.

E.                  Ventral-- (towards the) stomach.

F.                  Cephal-- (towards the) head.

G.                 Caudal-- (towards the) tail.

H.                 Superior-- above.

I.                    Inferior-- below.

J.                   Proximal-- close to body attachment (relates to appendages).

K.                Distal-- more distant from body attachment (relates to appendages).

L.                  Medial-- towards the midline (on torso or body).

M.               Lateral-- away from the midline (on torso or body).

N.                Superficial-- towards the surface.

O.                Deep-- away from the surface.

P.                  Supine (supination)-- palms facing ventrally in anatomical position.

Q.                Prone (pronation)-- palms facing dorsally in anatomical position.

R.                 Coronal (Frontal) plane-- separates dorsal from ventral in longitudinal plane.

S.                  Sagittal plane-- separates left from right, perpendicular to coronal in longitudinal plane.

1.                  Parasagittal plane-- sagittal plane not through the midline

2.                  Midsagittal plane-- sagittal plane through the midline.

T.                  Longitudinal plane-- runs in long axis of organism, coronal, and sagittal planes are longitudinal planes.

U.                 Transverse plane (cross section, x.s.)-- perpendicular to coronal and sagittal planes, cuts across longitudinal plane.

V.                 Horizontal plane--self-explanatory.

W.               Vertical plane-- self-explanatory.

X.                 Oblique plane-- any plane not as described above.

VII.            Animal metabolism is traditionally viewed as “cold blooded” or “warm blooded” but not that simple.

A.                 Ectothermic-- utilizes external environment for core temperature and uses behavioral mechanisms to maintain homeostasis (maintenance of a constant internal environment).

B.                 Endothermic-- utilizes physiological mechanism to maintain core temperature.

C.                 Heterothermic-- core temperature fluctuates.

D.                 Homoeothermic-- core temperature relatively constant.

E.                  Poikilotherm-- endothermic heterotherm (chipmunks, bats, others).

F.                  Some comments.

1.                  Ectotherms and heterotherms are traditionally viewed as cold-blooded.

2.                  Endotherms and homeotherms are traditionally viewed as warm-blooded.

3.                  There are numerous exceptions.

a)                  Great white sharks are ectothermic homeotherms--large size reduces surface area to volume ratio so heat does not radiate rapidly and heat retained.

b)                  Poikilotherms hibernate or undergo daily fluctuations to conserve energy-- temperature changes are physiologically driven.

I.                    The first Metazoan fossils appear as much as 800 ma in the Upper Proterozoic (Vendian) era of the Precambrian eon.

A.                 Metazoans represent a monophyletic clade, known as animals--multicellular heterotrophs, lacking a cell wall, and showing some level of cell specialization.

B.                 The ancestral Metazoan form is thought to have evolved from flagellated protozoans and produced three distinct animal clades (Subkingdoms): the Parazoa, Mesozoa, and Eumetazoa (discussed below).

C.                 The best-preserved mass of fossils of this age is found in the Ediacaria Hills of Australia.

1.                  This time period is referred to as the Edicarian epoch (of the Vendian or Upper Paleozoic period of the Precambrian era), and the animals of this time as the Ediacaria fauna or fossils.

2.                  The fossil bed appears to show impressions of jellyfish, corals, perhaps arthropods, and a group of unique organisms know as the Ediacaria of which nothing else is known.

II.                 There follows a significant gap in the fossil record for approximately 100 million years, until the beginning of the Cambrian period of the Paleozoic era of the Phanerozoic eon.

A.                 At the beginning of the Cambrian period there occurs an explosion of diversity of animal phyla.

B.                 Representatives of all animal “Phyla” evolve in this explosion of diversity, and many phyla that no longer exist.

C.                 The causes for this explosion are speculative.

1.                  It may be that oxygen levels were not high enough in deeper water.

2.                  There is evidence of significant glacial erosion of the continental masses leading up to the explosion.

a)                  This erosion may have delivered limiting minerals to aquatic and marine habitats sufficient to support diverse animal life.

b)                  This massive erosion may also explain the paucity of Ediacarian fossils, and the gap between them and the Cambrian explosion--they were eroded away.

D.                 The reality is that the “Cambrian explosion” was a “Proterozoic explosion” or “Ediacarian explosion.”

E.                  Relationships between the ancestral Bilateria are not clear, because there is not enough temporal distinction in the fossil record to determine the sequence of appearance of specific characteristics or organisms.

F.                  The probable relationships of animals that developed in the late Precambrian and early Cambrian will be considered with the animal classification that follows.

III.               The (Subkingdom) Parazoa includes the (Phylum) Porifera, and an obscure clade (Phylum), the Placozoa--as mentioned the Parazoa are not thought to be ancestral to the other animal clades (Mesozoa and Eumetazoa) as each evolved independently from a metazoan ancestor.

A.                 The (Phylum) Placozoa have the following characteristics.

1.                  They are small multicellular animals known from fish aquaria and shallow tropical waters.

2.                  They produce gametes and feed by phagocytosis or absorptive heterotrophy of protists.

3.                  Only two species are known.

B.                 The (Phylum) Porifera are sponges, and have the following characteristics.

1.                  Porifera are acoelomic, and asymmetrical (although some show radial symmetry).

2.                  Lack well developed tissues, organs, or organ systems.

3.                  Degree of cell specialization low, as cells are embedded in a gelatinous matrix called mesenchyme (or mesoglea or mesohyl).

a)                  Choanocytes.

(1)               Flagellated cells that line the spongocoele of sponge creating a flow of water through porocytes and out the osculum

(2)               The choanocytes filter water for organic debris which they phagocytize and transfer nutrients to other cells.

b)                  Epidermal (pinacocytes) or pinacodermal cells line the outer and inner surfaces of the sponge—not a true epithelium, lacks a basement membrane.

c)                  Amoebocytes secrete spicules, spongin, and probably mesenchyme, and may also form gametes in some sponges.

d)                  Porocytes allow water to enter the spongocoele.

e)                  Spongocoele (atrium)-- internal chamber of a sponge, not a digestive tract.

f)                    Osculum--Opening of spongocoele.

4.                  There are three basic body plans in the Porifera.

a)                  Asconoid sponges have a large single spongocoele.

b)                  Syconoid sponges have side chambers to the central spongocoele.

c)                  Leuconoid sponges have side chambers coming off the spongocoele’s side chambers, and are the most complex type of sponge.

5.                  Classification is based on a “skeleton” composed of structures called spicules, and presence of an elastic protein called spongin.

a)                  The spicules are of specific composition, and act as an internal support structure for cells of the sponge.

b)                  The spicules are secreted by amoebocytes.

c)                  Spongin is an elastic protein that gives a commercial sponge its “spongy” texture.

6.                  Poriferan clades (Classes).

a)                  Calcarea

(1)               Calcareous sponges.

(2)               Spicules of calcium carbonate.

(3)               Scypha and Grantia are genera.

b)                  Hexactinellida

(1)               "Glass sponges" fused spicules are composed of silicon.

(2)               Spicules are six pronged.

c)                  Desmospongidae

(1)               "Bath sponges" have spicules of unfused silicon, with spongin (a protein).

(2)               Commercial sponges or bath sponges are the spongin skeletons of desmospongids.

d)                  Sclerospongidae--"hard sponges" have spicules of silicon, with a “shell” of calcium carbonate, are deep-water sponges.

7.                  Reproduction in sponges.

a)                  Most can reproduce asexually--a small piece will grow into a complete sponge, and some produce structures called gemmules, which are masses of cells that grow into a new sponge.

b)                  Most are also hermaphroditic, choanocytes divide to produce sperm, or and choanocytes or amoebocytes form ova.

c)                  Sperm will fertilize ova in the mesenchyme and develop into ciliated amphiblastula larvae.

d)                  The amphiblastulae break into the spongocoele and swim out the osculum.

IV.              Members of the Subkingdom Mesozoa are tiny, internal parasites of marine invertebrates.

A.                 The ancestry of mesozoans is not well established; we are considering them as early animal forms.

B.                 Some zoologists actually consider them to be derived from flatworms (Platyhelminthes) in a “retrograde” form.

C.                 The Mesozoa is probably not a monophyletic clade.

V.                 The Subkingdom Eumetazoa includes all other animal phyla.

A.                 They exhibit characteristics of embryonic development discussed previously.

B.                 They have a true epithelium, with a basement membrane (discussed later).

VI.              The ancestral Eumetazoan is thought to have produced two distinct clades (Superphyla), the Radiata and the Bilateria.

A.                 The Superphylum Radiata are diploblastic, show radial symmetry, and contains the following phyla.

1.                  Phylum Cnidaria, which includes hydras, jellyfish, anemones and corals.

2.                  Phylum Ctenophora, know as comb jellies.

B.                 The Superphylum Bilateria includes all other animal phyla.

1.                  They show bilateral symmetry (except for the Echinodermata).

2.                  They are triploblastic.

VII.            (Phylum) Cnidaria (formerly coelenterata--coelenterates would be synonymous with Cnidarians) are members of the Radiata with the following characteristics.

A.                 Examples--jellyfish, sea anemones, corals.

B.                 Demonstrate radial symmetry.

C.                 Show tissues but not well developed organs.

D.                 Diploblastic.

1.                  They have an outer layer of cells (ectoderm), and inner layer of cells (endoderm).

a)                  The epidermis is the outer layer of cells derived from the ectoderm and includes the following cells.

(1)               Musculoepithelial cells--these are covering cells with contractile properties accounting for movement and prey capturing capabilities.

(2)               Nerve cells, which form a nerve net just beneath the epidermis--allow for coordinated movement and response to environment.

(3)               Ocelli--clusters of light sensitive nerve cells.

(4)               Cnidocytes--stinging cells that contain nematocyts that sting or entangle prey (see below).

b)                  The endodermis forms the inner layer of the digestive tract, secreting digestive enzymes into coelenteron.

2.                  Between the two layers is a layer of secreted protein called the mesoglea (the "jelly" in jellyfish)--the nerve net and ocelli may be found within the mesoglea.

E.                  Possess a large closed digestive sac called the coelenteron--is not a coelom.

F.                  All members possess cnidoblasts (cnidocytes).

1.                  Cnidocytes contain a capsule called a nematocyst.

2.                  The nematocyst contains a coiled tube that explodes out of the cnidocyte in response to touch.

3.                  The coiled tube contains a toxin that can range from relatively harmless to deadly (Portugese Man-o-War).

4.                  Nematocysts can only be used once.

5.                  Some flatworms and molluscs are able to eat cnidarians without discharging the nematocysts--they actually transfer the cnidocytes from the intestinal tract to other body regions where they use the cnidoblasts for protection.

G.                 There are two body forms.

a)                  Polyp--cylindrical, sessile (benthic), little mesoglea, anemones and corals.

b)                  Medusa--pelagic (swimming), posterior mouth, thick mesoglea, jellyfish.

c)                  Many Cnidarians show both forms during their life cycle.

H.                 Cnidarian clades (Classes).

1.                  (Class) Hydrazoa--polyp, fresh water, have stinging tentacles, sessile, some form complex colonies examples: Hydra, Obelia, Physalia (Portugese man-o-war).

2.                  (Class) Scyphozoa--jellyfishes, medusa, free swimming (pelagic), phototropism (possess ocelli--light sensitive).

3.                  (Class) Anthozoa (flowering animals)--corals, and anemones.

I.                    Sexual reproduction of jellyfish (our “type specimen”).

1.                  Eggs and sperm produced by adult medusae within “testes” and “ovaries” and released into water where fertilization occurs.

2.                  The zygote divides and forms a larva called a planula--a ciliated free-swimming stage.

3.                  The planula swims, eventually settles to ocean floor, and develops into a feeding polyp form called a Scyphistoma.

4.                  The Scyphistoma begins to section itself into several medusae, and is called the Strobila in this stage.

5.                  Medusal forms develop from the Strobila, dislodging themselves and, swimming off to eventually mature into adult medusae.

VIII.         The (Phylum) Ctenophora (comb jellies) are also within the Radiata and have the following characteristics.

A.                 They were once classified within the Cnidaria, but lack cnidocytes.

B.                 Jellyfish-like in appearance, but swim by means of eight rows of specialized ciliated cells called comb rows.

C.                 Ctenophores have adhesive cells for capture of small invertebrates, on long tentacles.

D.                 Mouth is anterior rather than posterior.

E.                  Most are bioluminescent.

IX.              Relationships within the Bilateria clade are not clear, because there is not enough temporal distinction in the fossil record of this age, to determine the sequence of appearance of specific characteristics or organisms--the remaining animal phyla are all in the clade Bilateria.

X.                 The Acoelomates are triploblastic and have no body cavity within mesodermal tissue.

A.                 An ancient acoelomate is probably ancestral to both the Pseudocoelomate and Eucoelomate clades that will be discussed later

B.                 Some Acoelomate Phyla are probably “retrograde” phyla that evolved from Psedocoelomates or Eucoelomates.

C.                 The Acoelomates do not, then, form a monophyletic clade.

D.                 Examples of Acoelomate clades (Phyla) are discussed below.

1.                  (Phylum) Platyhelminthes.

a)                  Common name--the flatworms.

b)                  General characteristics of the phylum.

(1)               These and all phyla that follow are triploblastic.

(2)               Acoelomic.

(3)               Closed digestive system, when present.

(4)               Excretory system present.

(a)                Flagellated cells called flame cells move fluids through excretory canals.

(b)               This fluid movement helps remove nitrogenous wastes.

(5)               Nervous system.

(a)                Most exhibit cephalization that includes an anterior ganglion.

(b)               “Nerve ladder” type of nervous system.

(6)               Reproductive system.

(a)                Most hermaphroditic.

(b)               Most have copulatory organs and practice internal fertilization.

c)                  Clades (Classes) of the Platyhelminthes.

(1)               (Class) Turbellaria--the free living flatworms.

(a)                Example Dugesia, a “Planarian.”

(b)               Ocelli clustered into "eyespots" that look like eyes, but are only light sensitive.

(c)                Locomote via cilia on bottom surface--"glide" over mat of mucus they secrete.

(2)               (Class)  Trematoda known as “flukes”.

(a)                Subclass Digenea (lack hooks, two suckers).

(i)                  All members parasitic.

(ii)                Parasites infect their hosts.

(a)                Intermediate host--host parasitized by a larval (immature) parasite.

(b)               Definitive host--host where parasite is sexually mature (reproductive).

(c)                Accidental host--not the typical host.

(iii)               Examples.

(a)                Opisthorchis sinensis--Chinese liver fluke.
Adults in human liver and intestine-- worms copulate, fertilizing eggs--eggs in feces, eggs hatch in water or consumed by snail--miracidium larva burrows into soft tissue--develops into cercaria larva which burrow out of the soft tissue into water--cercariae find fish, burrow into muscle and encyst--poorly cooked fish, and encysted larva, ingested by human--metacercariae excyst and develop into adults in intestine.

(b)               Schistosoma mansoni (and japonicum)--blood fluke.
Adults in blood vessels of intestine--female sits in groove of male (male larger) an the two “fused” together, so female eggs fertilized as flayed by male--migrate to vessels of rectum lay eggs--hooked egg breaks capillaries into rectum lumen--eggs in feces--miracidium larva into snail--develops into cercaria larva--cercariae burrow out of snail--swim to human and burrow through skin into bloodstream--migrate to vessels of intestine and mature.

(b)               Another Subclass, the Monogenea, is also recognized.

(i)                   They have hooks associated with the suckers.

(ii)                Mostly parasites on the gills of freshwater fishes.

(3)               Class Cestoda--tapeworms.

(a)                All members parasitic.

(b)               Body plan.

(i)                  Scolex

(ii)                Neck

(iii)               Strobilus composed of proglottids.

(a)                Each proglottid is a reproductive unit, capable of producing thousands of eggs.

(b)               Copulation may be internal with one proglottid of one worm fertilizing proglottid of another worm.

(c)                Obtain nutrition by directly absorbing digested molecules from intestinal tract.

(d)               Tapeworms can be several feet long.

(e)                Examples.

(i)                  Taenia saginata--human beef (sheep, pork, fish) tapeworm.
Adults in intestine--eggs in feces--eggs ingested by cow--eggs hatch in intestine, larva burrows into bloodstream to muscle tissue--form “bladderworm” larval stage in muscle--human ingests poorly cooked meat--excyst in intestine

(ii)                Dipyllidium caninum--dog tapeworm

(a)                Adult worms in dog intestine--eggs in feces--ingested by flea larva--flea matures, worm larva encyst in flea muscle--dog eats flea in grooming--larva excyst in intestine.

(b)               Humans can become accidental hosts if ingest flea parts by accident.

2.                  Phylum Nemertea (Rhynchocoela)

a)                  Common name--proboscis worms.

b)                  Possible intermediate in evolution between the Acoelomates and Pseudocoelomates due to presence of an open digestive system.

c)                  Triploblastic, acoelomic, open digestive system (as will all other phyla that follow).

d)                  Resemble flatworms but usually have an extendable feeding structure use to capture prey.

XI.              The Pseudocoelomate clades (Phyla) have a body cavity that is lined by mesoderm on the surface adjacent to the body wall, but the surface of body organs are not lined by mesodermal tissue (muscle or connective tissue).

A.                 Pseudocoelomates probably evolved from Acoelomate ancestors.

B.                 Pseudocoelomates are probably not a monophyletic clade.

C.                 The Pseudocoelomates are sometimes called the Ascelminthes.

D.                 Examples of Pseudocoelomate clades (Phyla) are discussed below.

1.                  Phylum Nematoda.

a)                  Common name roundworms.

b)                  One of the most numerous animals in terms of sheer numbers.

c)                  Numerous free living and parasitic forms--many plant parasites, as well.

d)                  Typically dioecious.

e)                  Males bear spicules, structures to hold and copulate with female worms.

f)                    Examples of parasitic nematodes.

(1)               Trichinella--causes trichinosis, common in rodents and pigs, humans occasionally from eating poorly cooked pork--Adults in intestine--female bears larva--larva abandon intestine and burrow into blood vessels of intestine--migrate to skeletal muscle (and joints) and encyst--next host ingests larva by eating raw or poorly cooked muscle.
Rats and mice cannibalize each other, pigs may prey on rats or mice or eat suffocated rodents in grain, and humans eat poorly cooked pork.

(2)               Enterobius--pinworm, common in children
Adult worms in rectum--female migrates to anus and lays eggs--eggs ingested by next or same host.

(3)               Ascaris--normally parasite of pigs.
Adult worms in intestine--eggs in feces--eggs ingested by next or same host--larva hatch, escape stomach and intestine by moving into bloodstream--migrate to lung enter air spaces--crawl up trachea--larva swallowed into stomach--mature in intestine.

(4)               Ancylostoma (Necator)--hookworm, common in children in Southern U.S.
Adult worms in intestine--larva in feces--larva in soil--burrow through skin into bloodstream--migrate to lung enter air spaces--crawl up trachea--larva swallowed into stomach--mature in intestine.

2.                  Phylum Gastrotricha--common predator in freshwater ecosystems.

3.                  Phylum Rotifera-- common predator in freshwater ecosystems, two large circular masses of cilia for feeding and locomotion.

4.                  Phylum Acanthocephala--intestinal parasite with spiny proboscis.

5.                  Phylum Nematomorpha-- “horsehair worms”

XII.            The first Eucoelomates to evolve were protostomate animals that evolved from the Acoelomates.

A.                 There are coelomic clades of animals that are not monophyletic with the Eucoelomates but we will not be considering any of those phyla, so we will consider the Eucoelomates to be monophyletic, but realize that perception depends on which phyla one considers.

B.                 The same is also true of Protostomates--we will consider them to be a monophyletic clade, and examples of Protostomate clades (Phyla) are considered below.

C.                 (Phylum) Mollusca are an ametameric branch of Protostomes.

1.                  Common name, the soft bodied animals.

2.                  General characteristics.

a)                  Lack segmentation, or metamerization, in embryonic development.

b)                  Well-developed (open) circulatory system, with a heart.

c)                  Well-developed nervous system--octopus is the most intelligent invertebrate.

d)                  Virtually all members possess the following:

(1)               A radula--a rasp-like plate in mouth used for scraping food; in some is highly modified (may be harpoon, with toxin in some predatory snails).

(2)               Mantle--a layer of cells that secrete a shell (calcium carbonate), and create a mantle cavity that contains gills and siphons.

(3)               Foot--a muscular organ used for locomotion.

(4)               A visceral mass--well developed organs.

3.                  Clades (Classes) of Mollusca.

a)                  Monoplacophora--single shell, rare unlike gastropods.

b)                  Caudofoveata--wormlike, rare, burrowing.

c)                  Solenogastres--rare, wormlike, pedal groove for locomotion.

d)                  Gastropoda (stomach-footed)--snails, slugs.

e)                  Pelecypoda/Bivalvia (spade-footed)--clams, oysters, shipworms.

f)                    Polyplacophora--chitons, have eight overlapping plates.

g)                  Scaphopoda (tusk-footed)--shell open at both ends, shell looks like tooth or tusk.

h)                  Cephalopoda (head-footed)--octopuses, squid, cuttlefish.

4.                  Reproduction.

a)                  Most are dioecious (separate sexes).

b)                  Bivalves release sperm and ova into water for external fertilization.

c)                  Most show a trochophore larva (ring of cilia around midbody for locomotion) and veliger larva (circular mass of cilia shifted to one side).

d)                  Some freshwater clams produce glochidia larva--small clamlike larva with teeth that are parasitic on fish gills.

D.                 Phylum Annelida.

1.                  Common name--the segmented worms.

2.                  General characteristics of the phylum.

a)                  Triploblastic, coelomic, open digestive system, protostomate, good circulatory, etc.

b)                  Distinguishing feature is they demonstrate metamerization-- body is divided into definite segments, called somites or metameres, which may aide in body organization.

c)                  Segments are divided internally by septa.

d)                  Segments possess bristles called setae, needed for locomotion.

e)                  Most show trochophore larva in reproduction (ring of cilia around midbody for locomotion).

f)                    Well-developed circulatory system.

3.                  Classes of Annelida.

a)                  Oligochaeta (few setae)--earthworms.

(1)               Enlarged region called a clitellum--closest to anterior end.

(2)               Some Australian and South American species grow 4-5ft.

(3)               Most hermaphroditic.

(4)               Reproduction.

(a)                Mucous sac (cocoon) produced by clitellum as worms mate.

(b)               Worms crawl past one another in opposite directions.

(c)                Sperm released from sperm ducts flow along seminal grooves to seminal receptacles of other worm.

(d)               Eggs and stored sperm of each worm deposited into mucous sac where fertilization occurs.

b)                  Polychaeta (many setae)--polychaetes.

(1)               Mostly marine, in sand and mud.

(2)               Most numerous annelid.

(3)               High diversity--thousands of species.

(4)               Have specialized appendages on each segment for gas exchange and locomotion called parapodia.

(5)               Used in environmental studies--changes in polychaete populations good indicator of effects of pollution.

(6)               For some, eggs and sperm released into water, others copulate by a variety of bizarre techniques, where fertilization occurs.

c)                  Hirudinea--leeches.

(1)               Posterior sucker for attachment.

(2)               Feed with mouth, not posterior sucker--slice skin, suck blood.

(3)               Reproduction similar to oligochaetes.

E.                  Phylum Onychophora-- “walking worms”

1.                  Tropical predator in leaf litter may be a link between annelids and arthropods.

2.                  They show a mixture of annelid and arthropod traits.

a)                  They have walking appendages, but lack a jointed exoskeleton.

b)                  They have antennae.

c)                  Body is soft and segmented like annelids, but is chitinous.

d)                  Heart is like arthropods.

F.                  Phylum Arthropoda.

1.                  Common name is the joint footed animals.

2.                  Characteristics of phylum.

a)                  Distinguishing feature is presence of a chitinous, jointed exoskeleton.

b)                  Same characteristics as above concerning circulatory, nervous, etc., etc.

c)                  They show some external segmentation.

d)                  Complex sensory organs, and nervous system, although are invertebrates.

e)                  Complex muscular system.

f)                    The exoskeleton is not cellular, cannot grow, must be shed (molts) and replaced.

g)                  Some will molt several times in life.

h)                  Many exhibit complex social behavior--bees, ants, and termites.

3.                  Subphylum Trilobita--fossil trilobites, all members extinct

4.                  Subphylum Chelicerata

a)                  General characteristics.

(1)               Lack antennae.

(2)               Usually two pairs of oral appendages that are variously modifi