gene

Chapter 11. The control of gene expression
Every cell must be able to translate a gene into a protein, but must also be able to regulate when particular genes are used
Cells control the expression of their genes by saying WHEN individual genes are to be transcribed
E. coli can use lactose (the sugar in the milk) as food because it has the genes that code for the enzymes that will use the lactose.
However, E. coli needs these enzymes only when lactose is present, otherwise it is a waste of energy.
Therefore, how can E. coli regulate gene expression?
In E. coli genome, there are 3 genes that encode for the 3 enzymes necessary to use lactose
These genes are one after the other. Just before the genes, there is a DNA region which is
a control sequence (Fig. 11.1B).
One piece of this sequence is called PROMOTER, where RNA polymerase binds to the DNA & starts transcription.
Between the promoter & the genes there is a region called OPERATOR, and it acts as a switch
Promoter, operator & genes are called OPERON (exists only in prokaryotes)
Just before the operon there is a regulatory gene (always expressed) that encodes for the repressor. The REPRESSOR, in its active state, binds to the operator & does not allow the RNA polymerase to attach and transcribe the genes.
BUT, when lactose is present, it binds to the repressor and the repressor becomes INACTIVE
This means that it does not attach to the operator anymore and the RNA polymerase can bind to the promoter and start transcription.
When the lactose is not present anymore and it has all been used, the repressor becomes active again and the gene expression stops.
Also, we can have the opposite situation
The lac operon is active ALONE and inactive with lactose, but there are other cases with the opposite situation: e.g. trp operon in E. coli.
E. coli is able to synthesize trp by itself, using enzymes encoded by the trp operon
When trp is available in the environment it will stop making it & use the available one.
In this case the trp repressor is INACTIVE in absence of trp, when the cell needs to make it; if trp is present, it binds to the repressor (Fig. 11.1C)
In this way the repressor becomes ACTIVE, binds to the operator and stops gene expression.
Also, there enzymes called ACTIVATORS, which turn on the operons when they bind to the DNA. They help RNA polymerase to attach to the promoter & start transcription.
Gene regulation in eukaryotes
In eukaryotes gene regulation is even more important & much more complex than for prokaryotes
This is because most eukaryotes are multicellular organisms with different tissues
A skin cell has the same DNA than a brain cell or a liver cell, so how come that they look so different?
They express different genes, just what they need to perform their functions.
However, with few exceptions, they keep all their DNA, so potentially they can still express all the other genes (Fig. 11.4).
e.g.: Dolly, the cloned sheep (Fig. 11.3B)
She is the result of a sheep egg, devoid of its nucleus & to which it has been transplanted a nucleus from a sheep mammary cell, which is a very specialized cell. The egg was put in the uterus a sheep and it developed in a normal, entire animal
First way of controlling gene expression is DNA packing (Fig. 11.5A)
In eukaryotes DNA is associated with small proteins, the HISTONES. DNA + histones are tightly packed (coiled and folded). This DNA packing can prevent gene expression because for a gene to be transcribed the histones must loosen their grip on the DNA. A cell may use higher level of packing for long term inactivation of genes
In eukaryotic cells, most genes are turned off by default (activator proteins are more important than repressors).
Gene transcription involves not only RNA polymerase but enzymes called TRANSCRIPTION FACTORS. They bind to DNA regions called ENHANCERS, far away from the gene. These proteins bend the DNA and help RNA polymerase attach to the promoter and start transcription (Fig. 11.6).
After transcription is completed, in eukaryotic organisms the mRNA is processed. Before moving from the nucleus to the cytoplasm, the mRNA is elaborated.
A cap and a tail are added at the ends (protect the mRNA from being attacked by enzymes and will help the ribosomes to recognize it). Most eukaryotic genes include non-coding regions, i.e. meaningless regions. Before going to the cytoplasm the mRNA is SPLICED, i.e. the non coding regions (INTRONS) are cut off, and only the coding regions (EXONS) will be kept. Introns are another way to regulate gene expression (Figs. 11.7A and 11.7B)
In eukaryotic cells also translation is subject to regulation. The life-time of an mRNA molecule is one factor regulating how much protein is produced. Long-lived mRNA are translated much more than short-lived ones.Translation can be regulated by inhibitor proteins. Also after translation there are regulation mechanisms: e.g. hormone insulin is translated as a long protein, but only when it's cut it becomes active. The life-time of a protein is another way of regulating gene expression (Figs. 11.8A and 11.8B).
Gene regulation in eukaryotes: summary (Fig. 11.9)
DNA packing Presence of activator proteins mRNA processing: splicing and addition of cap and tail Life time of mRNA Translation: presence/absence of inhibitors Modification/activation of the protein Lifetime of the protein
Why is gene regulation important
1) Embryonic development
cascade of gene expression and cell to cell signaling is responsible of correct development of the embryo
e.g. in insects as well as in mammals: there are genes called HOMEOTIC GENES that determine what body parts develop when and where
e.g. one set of genes in the fruit fly instruct the segment of the head to form antennae. Elsewhere these genes are turned off (Fig. 11.10B)
Development of cancer
Cancer develops when the cell cycle is altered, i.e. when the cell have an uncontrolled growth
How can this happen?
Cancer develops when changes to some cells' genes or changes in the way certain genes are expressed occur. These genes are called oncogenes, and can make the cell cancerous. A normal gene with the potential to become an oncogene is called proto-oncogene.
Normally these genes code for growth factors or are involved in cell growth. When these proto-oncogenes undergo mutation, they can become oncogenes: normally when this happens they produce a hyperactive protein that stimulates uncontrolled cell growth -> the cell becomes cancerous.
Or, the promoter can undergo mutation, so the gene is expressed in excess (Figs. 11.13, 11.14A and 11.14B).
Changes in genes that inhibit cell division are also involved in cancer. Any mutation in these genes (called TUMOR-SUPPRESSOR GENES) that cause a malfunctioning of their product may help cancer develop
How does cancer develop?
Mutations normally occur after exposition to mutagens.
Mutagens: X-rays, UV-rays, many chemicals, some viruses
Normally more than one mutation is needed to cause cancer, that's why prolonged exposition to mutagens helps develop cancer (Figs. 11.15A and 11.15B)
Why cancer is so dangerous? Because with this excessive growth the organs cannot work well
Smoke and lung cancer.
Cigarette smoke has some 3,000 chemicals such as vinyl chloride, benzo(a)pyrenes & nitroso-nor-nicotine, all potent mutagens.
Of every 100 American college students who smoke cigarettes regularly: 1 will be murdered, about 2 will be killed on the roads, and about 25 will be killed by tobacco.
End of Chapter 10: Viruses
VIRUSES
Made of a protein coat and DNA (or sometimes RNA). Phage viruses (infecting bacteria) can insert their genes in the bacterial genome without killing the bacteria.
Some pathogenic bacteria cause the disease only because the viral genes direct the bacteria to produce toxins that make people ill (e.g.: diphtheria, botulism, scarlet fever).
Viruses can reproduce only by infecting cells.
The host cell provides most of the components necessary for replicating, transcribing and translating the viral nucleic acid.
However, a virus can have two different ways to reproduce:
1) Lytic cycle
Viral DNA in host; viral DNA circularizes; viral DNA is replicated many times; viral proteins are synthesized; viruses assemble. They break the host cell and go to infect new cells (Fig. 10.17)
2) Lysogenic cycle
Viral DNA in host; viral DNA circularizes; viral DNA is inserted into bacterial chromosome by recombination; bacterium reproduces normally, replicating viral DNA with its own DNA; eventually viral DNA leaves the chromosome and goes into lytic cycle (Fig. 10.17)
VIRUSES WITH RNA
Some viruses have RNA instead of DNA as genome (e.g.: influenza, measles, mumps, polio and AIDS viruses) (Fig. 10.18A and 10.18B)
The virus attach to the cell membrane; RNA with protein coat enters the cell; enzymes remove protein coat; RNA is copied; new RNA used for synthesis of viral protein and as template for new viral genome; the new proteins assemble around the new RNA; the virus leaves the cell to infect new cells
HIV virus (AIDS)
HIV virus is a special type of RNA virus, called retrovirus. It is able to produce DNA from a RNA template. It has an enzyme called reverse transcriptase, which synthesizes DNA from an RNA molecule (Figs. 10.21A)
The virus enters the cell; the reverse transcriptase uses the RNA as template to make a DNA strand; it makes a second, complementary strand of DNA; this double stranded DNA enters the cell nucleus and inserts itself in the chromosomal DNA. It can stay there for long time; eventually the viral DNA is transcribed into RNA and translated into viral protein.
New viruses assemble, leave the cell to infect other cells (Fig. 10.21B)
Why is so difficult to fight AIDS (and the flu)?
RNA viruses have a very high rate of mutation because they do not have the proofreading steps of the DNA replication
Some mutations may enable existing viruses to evolve in new varieties, resistant to drugs and to the immune system of people that have developed immunity to the ancestral virus
Chapter 12. DNA technology
Bacteria and DNA manipulation.
Bacteria do not have meiosis, but they have several ways to produce new gene combinations
The bacterial DNA is normally found in only one circular chromosome
Some bacteria can have additional DNA in a single, circular molecule, separate from the chromosome: this is called PLASMID
PLASMIDS are "extra" DNA that contain few genes. Usually plasmids are not essential for survival, but they may possess genes that may benefit the bacterium (i.e. resistance to antibiotics)
Bacteria do not have meiosis, but they have several ways to produce new gene combinations
1) transformation: bacteria can incorporate foreign DNA from the surroundings e.g. Griffith's experiment with pneumonia-causing bacteria (Fig. 12.1A)
2) transduction: bacteriophages (viruses attacking bacteria) can transfer bacterial genes from one bacterium to another. This happens when a fragment of DNA of a phage's previous host is accidentally packaged within the phage's coat instead of phage DNA. When the phage infects a new bacterial cell the former host's DNA is injected into the new host (Fig. 12.1B)
3) conjugation: or "sex" in a bacterial world. 2 bacterial cells come in contact, one acting as a donor cell ("male"), the other as a recipient ("female"). Normally a bacterium acts as a "male" if it has a specific piece of DNA, called the F-factor. This F-factor carries the genes to make sex pili, and also has an origin of replication, where DNA replication can start (Figs. 12.1C, 12.1D)
The "male" bacterium, when gets in touch with a recipient, forms sex pili and one of them attaches to the "female" cell. The cell membranes fuse, a cytoplasmic bridge forms and the male chromosome starts to replicate at the origin of replication. The copy is then transferred to the recipient cell through the cytoplasmic bridge. Once inside the female cell, crossing over can occur (Figd. 12.2A and 12.2B)
Some bacteria can have additional DNA in a single, circular molecule, separate from the chromosome: this is called PLASMID (Fig. 12.2C)
PLASMIDS are "extra" DNA that contain few genes. Usually plasmids are not essential for survival, but they may possess genes that may benefit the bacterium (i.e. resistance to antibiotics)
DNA technology and genetic engineering found in plasmids one of their most powerful tools.
WHY?
One of the greatest discovery of this century is the discovery of restriction enzymes in bacteria ( Nobel prize in 1978, Nathans and Smith)
These enzymes protect the bacterium against intruding DNA from other organisms or phages. The restriction enzymes cut the foreign DNA in pieces so that it can not harm the cell.
The bacterium has modified its own DNA to protect it from these enzymes
So, if we cut a plasmid with restriction enzymes, we will have pieces of plasmid DNA.
If we have pieces of other DNA (from another source) cut with the same enzymes, they will have complementary sticky ends. Therefore, they will stick together by base pairing. This union can be made permanent by the enzyme DNA ligase. The final outcome is a recombinant DNA, i.e. a DNA molecule carrying a new combination of genes (Figs. 12.3 and 12.4).
Then the recombinant plasmid is incorporated into bacteria via transformation and allowed to multiply (Fig. 12.5).
This technique has MANY APPLICATIONS
Examples: most hormones (for medications) are produced in this way: insulin for diabetics, growth hormone for children affected by dwarfism, etc. (Fig. 12.22A)
In this way special bacteria are engineered to clean up toxic wastes, to produce genetically engineered plants etc.
However, for bacteria engineered to express eukaryotic genes (e.g. insulin) the target gene has to be synthesized.
The mRNA corresponding to the insulin gene is isolated, the enzyme reverse transcriptase is added (it makes DNA from an RNA template) and the DNA is synthesyzed (Fig. 12.7)
What's the difference?
Eukaryotic genes have introns in the gene, i.e. not expressed pieces of DNA. The mRNA is spliced before being translated.
But prokaryotes (i.e. bacteria) are not able to splice the mRNA since their genes do not have introns. Therefore if we want to express a eukaryotic gene in a bacterium, we have to take off the introns (Fig. 12.7)
Restriction enzymes have other powerful applications, if combined with other techniques
One of these technique is gel electrophoresis, a method to sort macromolecules by electric charge and size.
DNA has a negative charge due to the phosphate group. So, if placed in an electric field with a ­ pole and a + pole, the DNA will move toward the + pole (opposites are attracted) (Fig. 12.10)
How does gel electrophoresis work?
A porous gel is made and the DNA is poured into the gel. The gel is then covered with a special liquid (buffer) and an electric current is applied so that one end is ­ and the other one is +. The DNA moves toward the + pole, however, if there are different sized DNAs, the smaller pieces move faster than the bigger ones. At the end we will have different bands, corresponding to the different sized pieces of DNA.
How do we use this technique?
Our DNA is unique, with the exception of identical twins.
Here (Fig. 12.11A) we have two alleles of the same gene. These two alleles have 1 bp of difference. If we cut it with a restriction enzyme that cuts between the two C bases in the sequence CCGG, allele 1 has 2 sites, so it is cut twice. Allele 2 has only one site, so it is cut once. If we run on gel these fragments, we will have 3 fragments for allele 1 and only 2 fragments for allele 2 (Fig. 12.11B)
How do we use this technique?
e.g. in murder trial (Fig. 12.16A and 12.16B)
e.g. in paternity cases
Others: to detect harmful alleles in fetuses or children
Other techniques.
Polymerase Chain Reaction (PCR) (Fig. 12.12)
Small amount of DNA can be cloned (i.e. replicated) many times in vitro:
To the DNA, it is added the enzyme DNA polymerase, free nucleotides, and few other molecules and the DNA is copied millions of times in few hours.
This DNA can be used for sequencing (human genome project) and other application (analysis of DNA in mummified animals thousands of years old, etc.).
Automated sequencing: determination of nucleotide sequence in a particular gene or piece of DNA (Fig. 12.15)
Applications: Human Genome Project
Genetically engineered plants: recombinant plasmid is inserted in a bacterium that behaves like a virus in the lysogenic cycle: it is able to insert its genome into the host DNA. ((Fig. 12.19)
Applications: plants resistant to parasites, plants that grow faster, plants resistant to pesticides, etc.
e.g. transgenic salmon: the growth hormone gene is inserted in the fertilized egg directly in the nucleus to increase the fish growth
What are the possible negative effects of genetically engineered organisms?
Unknown side effects Allergies to g.e. food g.e. organisms can grow out of control and threaten the wild organisms (Fig. 12.21) Ethical issues
Chapter 13. How populations evolve
Evolution is the progressive change that occurs in organisms' characteristics through time
In 1831, the 22 year-old Darwin left England to go for a5-years' world trip with the Beagle (Figs. 13.1B and 13.1C).
At the time when he embarked on the voyage, the view of Darwin, and of his contemporaries, was that every species of organism had been created at the same time and had remained unaltered since then.
The current view at that time was that all organisms had been created at 9.00 a.m. on Sunday October 23 in 4004 B.C., as Archbishop James Ussher pronounced in the 17th century.
During his 5-year trip, Darwin saw things that made him change his mind.
e.g. in rich fossil deposit in Southern South America he saw fossils of extinct armadillos that were directly relate to the armadillos still living in the same area and yet different from those elsewhere.
Why would there be living & fossil organisms in the same place, directly related to one another, unless one had given rise to the other?
On the Galapagos islands, more than 1,000 Km off the coast of Ecuador, Darwin saw more than a dozen species of finches, all related but each specialized to catch food in a different way.
These finches more closely resembled S. American finches than any other, so perhaps an ancestral finch had been blown over the sea from S. America.
BUT... Since he saw many different species on the island, the birds must have changed AFTER they arrived!
In 1859 Darwin published the "On the origin of species" where he explains his theory on HOW evolution takes place
Evolution is DESCENT WITH MODIFICATION
Biological evolution can be defined as a change in the GENETIC characteristics of populations of organisms over time
A lot of evidence supports evolution
1) Fossil record
Fossils are the preserved remains of former living organisms. The fossil record contains excellent examples of how major new groups of organisms arose from previously existing ones (Figs. 13.2A-F)
One for all: Archaeopteryx

Found 2 years after Darwin's publication, it has many reptilian traits (e.g. teeth) and many bird-like features, like feathers
2) The study of biogeography and the theory of continental drift
3) Genetics and molecular biology (Fig. 13.3B)
4) Comparative anatomy and comparative embryology (Fig. 13.3A)
5) Direct observations of biological changes in populations (such as insect resistance to DDT and bacterial resistance to antibiotics)
ALL SUPPORT EVOLUTION
But HOW does evolution occur?
Before Darwin:
In early '800 French naturalist J. B. Lamarck suggested that the best explanation for fossils and the current diversity of life is that organisms evolve. He proposed that by using or not using its body parts, an individual tends to develop certain characteristics, which it passes on to its offspring
Lamarck's proposal is known as the inheritance of acquired characteristics
e.g. he suggested that the giraffe acquired its long neck because its ancestors stretched higher and higher into the trees to reach leaves and that the animal's increasingly lengthened neck was passed on to its offspring
This idea is wrong, but helped Darwin to develop his theory
Another key person for Darwin's insight was Thomas Malthus
Malthus published the book "Essay on the principles of population", where he claimed that humans (and all other species) tend to reproduce faster than food supplies, living space, and other resource can sustain.
The larger a population gets, the more people there are to reproduce in each generation. As population size burgeons, resources dwindle, so the struggle for existence intensifies.
But which individuals are the winners and losers?
Darwin observed that in a population the individuals are not identical, but they shows variations in size, coloration and other traits.
Darwin thought that variation in traits might affect an individual's ability to survive and therefore reproduce in particular environments
This process was called by Darwin NATURAL SELECTION
The essence of natural selection is unequal success in reproduction
Natural selection results in favored traits being represented more and more and unfavored ones less less in ensuing generations.
Thus the unequal ability of individuals to survive and reproduce leads to a gradual change in the characteristics of a population of organisms, with favored characteristics accumulating over the generations
e.g. peppered moths (Fig. 13.5B)
Strong support of Darwin's theory is found in artificial selection, the selective breeding of domesticated plants and animals (Figs. 13.4A and 13.4B)
Selecting individuals with the desired traits as breeding stock, humans are playing the role of the environment and bringing about differential reproduction
A population evolves, not an individual.
An individual may contribute to the evolution of the population, but itself it does not evolve
Evolution of a population is defined as a change in allele or genotype frequencies over generations
Allele is an alternate form of a gene
Most organisms are diploid, i.e. have 2 copies of chromosomes, one copy from the father and one from the mother. Therefore they have two copies of each gene
These two copies are called alleles
They can be identical or different (Fig. 13.14A)
If an individual has two identical alleles is called homozygous
If the two alleles are different it is called heterozygous
e.g. peppered moth (Fig. 13.5B)
Wing color is caused by one gene, with two alleles, W for black color and w for white
An individual can be: WW, Ww or ww
Before industrialization London's population had 1,000 moths:
700 were white (ww)
100 were black (WW)
200 were gray (Ww)
What's the allele frequency of this population?
Each individual has two alleles: therefore, to calculate the frequency (=%) of the W allele we have to take all the WW moths. Since each WW moth has 2 W alleles, we multiply the individuals x2. Also the Ww moths has W alleles, but in this case they have only one W. Therefore we take their number without multiplying it. We divide these numbers by the total, but since all the individuals have 2 alleles, we multiply the total x2.
W= (2*WW + Ww)/2*total = (2*100 + 200)/2*1000 = 400/2000 = 2/10 = 20% or 0.2
The same procedure is for the w allele
700 were white (ww)
100 were black (WW)
200 were gray (Ww)
w= (2*ww + Ww)/2*total= (2*700 + 200)/2*1000 = 1600/2000= 8/10= 80% or 0.8
So, the allele frequencies of this population is:
0.8 w
0.2 W
After industrial revolution, there are:
800 WW (black)
100 Ww (gray)
100 ww (white)
What's the allele frequency of this population, descendent of the former?
W= (2*800 +100)/2*1000 = 1700/2000 = 85% or 0.85
w= 1-W = 15% or 0.15
The allele frequency of the population changed over time -> the population EVOLVED
Let's assume we have a population that does not evolve: the allele frequencies of the population through generation must stay the same
This means that the population is in Hardy-Weinberg equilibrium
Hardy-Weinberg equation is a simple formula that allow us to predict genotype frequencies in a non-evolving population
H-W equation:
p2 + 2pq + q2 =1
p2 = frequency of genotype WW
2pq = frequency of genotype Ww
q2 = frequency of genotype ww
How do you apply the H-W equation? (Figs. 13.8B & 13.8C)
Our original moth population was:
700 white (ww)
100 black (WW)
200 gray (Ww)
With w=0.8 and W=0.2
You substitute p with W frequency and q with w frequency in the formula
p2 + 2pq + q2 =1
so it becomes
(0.2)2 +2(0.2)(0.8) +(0.8)2=1
0.04 (WW) + 0.32 (Ww) +0.64 (ww)
What are the causes of population evolution?
Mutation Migration Genetic drift Non-random mating Natural selection
or: a population in Hardy-Weinberg equilibrium when there is not:
Mutation Migration Genetic drift Non-random mating Natural selection
1) MUTATION
Mutation is a change in the nucleotide sequence of the DNA (Fig. 13.14A)
All evolutionary changes depend ultimately on mutations. However mutations occur so infrequently that they cause little direct change per generation in the allele frequency of a population
2 exceptions are:
HIV virus has a very high rate of mutations -> it becomes resistant to drugs very quickly
Resistance of bacteria to antibiotics
2) MIGRATION
Migration is the gain or loss of alleles from a population by the movement of individuals or gametes
i.e. migration of humans: America population before and after Columbus
3) GENETIC DRIFT
When the frequency of particular alleles changed drastically only by chance
One allele may be represented in only few individuals and these individuals do not reproduce or die
This happens in small populations only
One case that involves a population small enough for genetic drift is called FOUNDER EFFECT: when few individuals forms a new colony, these few individuals may have rare alleles (rare in the original population) that become common in the new population
Founder effect is important in the colonization of new islands (e.g. Galapagos and Hawaii)
Example of founder effect in humans: Amish
Each Amish community is descended from a small immigrant stock, as attested by the few family names in a community. In Pennsylvania only 8 family names account for 80% of the Amish families.
In these communities the Ellis-van- Creveld syndrome is very common. This disorder was introduced by one of its founders and persists today because of the reproductive isolation of the Amish
Another case involving genetic drift is the BOTTLENECK EFFECT: this happens when a large population is killed by a disaster (flood, heart quake, etc.) unselectively, producing a small surviving population that is unlikely to have the same genetic make-up as the original population (Fig. 13.11A)
e.g.: excessive hunting in cheetah populations in Africa (Fig. 13.16)
4) NON-RANDOM MATING
When individuals with a certain genotype mate with one another more frequently than expected by random basis
One example is INBREEDING, i.e. mating with relatives (ex. Amish, Mormons)
Inbreeding increases the proportions of individuals that are homozygous, so homozygotes are more frequent than predicted by Hardy-Weinberg
-> Recessive alleles become expressed
-> High rate of genetic disease
e.g.: Charles V (1500-1558), Emperor of Germany was affected by a deformity of the jaw.
The defect ran in the House of Hapsburg until very recent times because of the exceptional number of marriages between cousins (inbreeding effect)
5) NATURAL SELECTION
The environment determines which kinds of individual in a population are the most fit and more likely to successfully reproduce
3 types of selection
a) DIRECTIONAL SELECTION: one phenotype (genotype) is favored over the other
e.g. black moths after Industrial Revolution, DDT resistance in insects (Figs. 13.13.5A-B, 13.20, 13.21).
b) STABILIZING SELECTION: the heterozygote is favored over the homozygotes (Fig. 13.20)
e.g. sickle cell anemia in Africa.
In sub-Saharan Africa, where malaria is endemic, there is a high frequency of the sickle-cell-anemia allele, which confers resistance to malaria.
The homozygotes for sickle-cell anemia have the disease, therefore die of anemia.
The normal homozygotes are susceptible to malaria, so they probably die of malaria.
The heterozygotes are not anemic, but they are also resistant to the malaria parasite -> they are advantaged over both homozygotes.
Where malaria is not present, the heterozygote is not advantaged any more and the sickle-cell allele is quickly removed from the population
c) DISRUPTIVE SELECTION: when the heterozygote is less fit, the selection acts to favor both the homozygotes (Fig. 13.20)
e.g. snails (black, white and gray) that leaves in habitat where there is lava rock (black) and white sand. The gray snails are visible everywhere -> they are eaten more frequently and tend to be eliminated
Chapter 14. The origin of species
What is a species?
"If it looks like a duck, walks like a duck and quacks like a duck, then probably it's a duck"
Morphological species concept: based on morphological (i.e. phenotypic) traits
BUT... Morphology itself is not enough (Fig. 14.1B)
Biological species concept: a species is a population or a group of populations whose members have the potential to interbreed and produce fertile offspring (Fig. 14.2)
PROBLEMS: it is not applicable to asexual organisms; it is not applicable to extinct species or fossils
Evolutionary species concept: a species is a cluster of organisms that represent a genealogy, or lineage of descent.
It is based on finding unique features (genotypic or phenotypic) for the clusters and their lineages. It is alternate approach to reproductive isolation (biological species concept)
What causes reproductive isolation between two closely related species?
PRE-ZYGOTIC ISOLATION: it affects the parents
1) Mating or flowering occurs at different times. i.e.the Monterey pine releases pollen in February, the Bishop's pine releases its pollen in April -> TEMPORAL ISOLATION
2) Two species live in the same area but in different habitats. i.e. garter snakes: one species lives in the woods, another in the water -> HABITAT ISOLATION
3) There is no sexual attraction between the two species: the female like the courtship rituals of its own species and not those of another -> BEHAVIORAL ISOLATION (FIG. 14.3A)
4) The sex organs of the two species do not match so copulation do not occur -> MECHANICAL ISOLATION (Fig. 14.3B)
5) A male and a female may copulate but the gametes are not compatible, i.e. the sperm and the egg do not fuse and the zygote is not formed -> GAMETIC ISOLATION
POST-ZYGOTIC ISOLATION: it affects the offspring
1) The gametes fuse, but the hybrid do not survive -> HYBRID INVIABILITY
2) The hybrids of two species survive and reach maturity, but they are sterile -> HYBRID STERILITY (Fig. 14.3C)
3) The first-generation hybrids are viable and fertile, but then the offspring of next generation is feeble or sterile -> HYBRID BREAKDOWN
SPECIATION: GENERATING DIVERSITY
The tremendous diversity of life is caused by SPECIATION, the process in which one species splits to form two or more species that are reproductively isolated from each other
The crucial event in speciation is the evolution of reproductive isolation.
Usually, speciation is considered a secondary consequence of the evolutionary divergence of populations
Populations evolve genetic differences from one another ­for whatever reason- and some of these genetic differences have the accidental by-product of causing partial or total reproductive isolation
1) GEOGRAPHIC ISOLATION (Figs. 14.4 & 14.8C)
Speciation can occur when populations of a single species become physically separated from one another so that gene flow is hampered. This is called ALLOPATRIC SPECIATION
2) ADAPTIVE RADIATION (Figs. 14.5B &C)
When numerous species arise from a common ancestor introduced to new and diverse environments. i.e. colonization of islands, such as Galápagos (Darwin's finches) and Hawaii
3) SYMPATRIC SPECIATION
Reproductive isolation occurs in populations living in the same area, i.e. they are not physically isolated.
Quite rare among animals, but important in plant evolution
Example: speciation by way of polyploidy (Figs. 14.6A & 14.7A-B)
If during gamete formation meiosis fails to take place, the gametes will be diploid instead of being haploid.
The resulting zygote will therefore be tetraploid: that is, it has 4 copies of each chromosomes
Eventually, these tetraploids plants are able to breed with the diploid plants, but the hybrid will be triploid and therefore not fertile (odd number of chromosomes -> cannot form homologous pairs and separate during meiosis)
Examples of polyploid species:wheat, coffee, bananas, cotton, salmon, etc.
RATES OF SPECIATION
How long does it take for speciation to occur?
a) Populations evolve differences gradually as they become adapted to their local environments -> gradualist model (Fig. 14.8A)
b) Evolutionary changes occur abruptly, with the new species diverging from the ancestral lineage in a relatively brief time, followed by periods of little or no change (equilibrium) -> punctuated equilibrium model (Fig. 14.8B). Example of sudden speciation: polyploidy
POP QUIZ (solution)
In my yard last month there was the following population of snails:
33 were brown-shelled (xx)
88 were black-shelled (XX)
57 were gray-shelled (Xx)
a) What is the allele frequency of this population?
b) If they mate and produce a total of 187 babies, how many will they be brown, how many will they be black and how many will they be gray?
a) There are two alleles X & x, and 3 genotypes. To calculate the frequency of the X allele (see explanation above in the notes of Chapter 13)
(2*XX)+Xx/2*total -> (2*88)+57/2*178 = 233/356= 0.65 (or 65%)
x= 1-X= 1-0.65= 0.35
b) With the above allele frequencies, apply the H-W equation
p2 +2pq +q2
where p is the X frequency and q is the x frequency
(0.65)2 + 2*(0.65)*(0.35) + (0.35)2 = 0.422 +0.455 + 0.122
These numbers are the genotype frequencies in the offspring. It means that 0.422 (or 42.2%) of the babies will be black (XX), 0.455 (or 45.5%) will be gray (Xx) and 0.122 (or 12.2%) will be white (xx).
To get the actual number, multiple each percentage (frequency) for the total number of babies, and you will have
79 black (XX)
85 gray (Xx)
23 white (xx)
The total should match the total of the babies in the question (79+85+23 = 187). If not, you MUST round up.
A similar question will be present in the exam, so make sure you understand how to do it and bring a calculator
Life on Earth
Earth is about 4.5 billion years old
Life on Earth has been around for about 3.5 billion years
How did life (and Earth) changed during this time and how do we know it?
Fossil record: oldest fossil found so far is 3.5 b.y. old
Fossils of very weird creatures not existing any more
Geology and the study of rocks

Relative dating: something is older than something else but don't know how old.
e.g. if a fossil is found in a lower stratum than another, is then older than the other
Absolute dating: use of isotopic ratio in fossils.
Living organisms contain certain atomic isotopes in a definite ratio. When an organism dies, this ratio changes, and this value is used to know how long ago a fossil died (and therefore, how old is the fossil)
Wegener and the continental drift theory
In 1912, Wegener proposed that continents are not fixed, but they move around. The actual shape of continents results from the breakage of a super continent, the Pangea, when all land masses were together
At that time nobody believed him, but now we have evidence he was right.
Solid continents are lighter than the hot mantle beneath, so they float on it.
Two main forces cause the continental plates to move:
o Hot plumes of liquid rock can rise to the surface and push continents apart (e.g. in the middle of the Atlantic ocean)
o Where two continental plates collide, one can sink below the other (e.g. along the Pacific coast of South America and near San Francisco)

Time on earth is divided in 4 eras:
Archeozoic (Precambrian): 4.5 bya-570 mya
Paleozoic: 570-245 mya
Mesozoic: 245-65 mya
Cenozoic: 65 mya-present
Each era is characterized by very peculiar life forms, climate, tectonic movements etc.
Precambrian (Archeozoic): 4.5 bya-570 mya
Life arose about 3.8 bya. The photosynthetic organisms slowly but constantly caused the oxygen content of Earth's atmosphere to increase.
The first eukaryotes and the first multicellular organisms appear in this era (it took about 2 by for the eukaryotes to appear since life arose!)
Life only in water, with flat bodies. No many predators but herbivores and scavengers also known as Ediacaran fauna

Paleozoic (570-245 mya)
Cambrian (570-510 mya)
Something happened to the Ediacaran fauna (extinction, caused by what?)
Cambrian explosion: explosion of new life forms, with new body shapes (Burgess shale fossils).
Many fossils are missing body parts: they are not bad fossils, it's the result of hungry predators!
Predation arises
First vertebrates appears


Ordovician (510-440 mya)
More marine life evolves, especially reef organisms.
Warm shallow seas and moist atmosphere
First colonization of land (land plant) and first freshwater plants
Then Godwana moves toward South Pole Þ first glaciation known to us
Sea level drops, all shallow seas are drained
60% of genera became extinct (1st mass extinction at the end of Ordovician)
Silurian (440-410 mya) & Devonian (410-360mya)
Recovery of reef communities
Jawless fish common, first jawed fish appear

Life on land diversifies (coastal forests)
First vascular plants & first tetrapods
Then bang! Another mass extinction
Carboniferous (360-286 mya)
Several glaciations change sea level many times; during low sea level, formation of coal (and oil)
Appalachians are formed
All plants except flowering plants
Permian (286-245 mya)
Pangea


Lowest sea level EVER (100 m below present)
Mountain chains create different climates on land: hot and dry
Asteroid at the end of Permian:
BANG!!!!!!!!
Greatest mass extinction EVER: >90% of all living species disappeared
END OF PALEOZOIC
Mesozoic ( 245-65 mya)
Divided in Triassic, Jurassic and Cretaceous
Spectacular expansion in the range of global diversity:
o In the seas, invertebrates & fishes underwent adaptive radiation
o On land, gymnosperms, insects and reptiles became the dominant lineages
o angiosperms (flowering plants) appeared in Cretaceous (and became the ruling plants in almost all environments in about 40 my)
o in early Triassic first dinosaurs evolved, possibly warm blooded & small; first mammals and birds
o at the end of Triassic (205 mya) another mass extinction occurred (another asteroid??): 35% of all animal families died
Most animals that survived this mass extinction were smaller, and less vulnerable to drastic temperature changes
Jurassic and Cretaceous: the age of dinosaurs and gymnosperms
About 120 mya, temperatures increased greatly and Pangea started to break up (formation of Atlantic Ocean)

o Angiosperms appeared at the end of Cretaceous
o At the end of Cretaceous (65 mya) an asteroid the size of Mount Everest hit our planet: MASS EXTINCTION!
Dinosaurs and many marine organisms disappeared
Cenozoic (65 mya-present)
After the asteroid hit the Earth, climate changed
The breakup of Pangea provoked the formation of Andes, Himalayas and Alps.

Tropical forests were more extended than today

Mammals radiated quickly
In Eocene period (57-35 mya) subtropical forests were extended into the polar regions
In Late Eocene climate became cooler and drier
Mammals continue to radiate
In Oligocene (35-23 mya) origin of Apes
In Pleistocene (1.8-0.01 mya) humans appear; ice ages
About 12,000 ya overkill extinction in the Americas due to human migration from Beringia
Summary of life on earth
Precambrian: life arose, O2 in the atmosphere increases slowly. Eukaryotes appear after 2 by. Life only in seawater, weird animals, no predators
Sometimes (when?) these animals became extinct
Paleozoic: Cambrian explosion, predators appear; vertebrates appear; first land plants (440 mya). Godwana moves toward S. pole and climate changes. At the end of Ordovician (440 mya) mass extinction. During Silurian and Devonian radiation of marine life (fish appear) and land plants (vascular plants & tetrapods appear), then at the end of Devonian other mass extinction
In Carboniferous glaciations with swinging sea level Þ coal and oil formation. All plants are present but Angiosperms. In Permian Pangea is formed, very low sea level, different climates inland
Asteroid at the end of Permian: >90% of all life is gone: GREATEST MASS EXTINCTION EVER
Mesozoic: spectacular radiation of life both in water and on land
In early Triassic first dinosaurs (small) first birds and mammals. At the end of Triassic (205 mya) mass extinction. Surviving animals were small.
In Jurassic and Cretaceous big radiation of reptiles (dinosaurs) and gymnosperms; climate change (hot hot hot!) and Pangea starts to break up. Angiosperms shows up and radiate extensively
Asteroids at the end of Cretaceous: mass extinction!
Cenozoic: hot and wet. Formation of all major mountain chains due to movement of continents. Mammals radiate quickly as do the angiosperms. Tropical forests very extended
About 35 mya climate cools down, mammals take over
In the Oligocene Apes origin, in Pleistocene ice ages and humans evolve
Another mass extinction is going on today
__________________________________________________________________________________________
After each mass extinction, there has been an explosion of organisms, which radiated from the ones that survived the extinctions.
What enables some species to survive and proliferate when many others die?
Chance had definitely a major role
Organisms too specialized or with peculiar requirements are unfavored
Organisms with a broad tolerance range are favored
Some key adaptations may have helped some organisms better than others (e.g. warm-blooded mammals were favored over cold blooded dinosaurs after the asteroid impact)
Some adaptations may have got refined and turned out to be useful in other context (e.g. bromeliads) -> exaptations (Fig. 15.6)
A subtle change in a species' developmental program can have profound effects, e.g. a slowing of the development of some organs can produce a very different organism
Example: axolotl retains juvenile body features in the adult (Fig. 15.7A)
This phenomenon is called paedomorphosis
Humans are paedomorphic too
We have a period of life, childhood, which is peculiar to our species: in other species (mammals, birds, etc.) there is a period of infant dependency, when the young are fed and need parental protection. After this period, most species develop rapidly in adults.
Only humans have true childhood, a prolonged period between infancy and adolescence when we are still dependent on parental care. This may be necessary to provide more time to learn from adults.
Our skull is paedomorphic, i.e. retains fetal features even after maturity (Fig. 15.7B)
Trends in evolution of species are analogous to trends in evolution of populations.
Example: horses evolved from animals of small size, with 4 toes per foot. Modern horses are big and have only one toe per foot.
Why did this happen?
Species are analogous to individuals: speciation is their birth and extinction is their death. Unequal survival of species results in their evolutionary trends (Fig. 15.8)
The evolutionary history of a group is called phylogeny.
The evolutionary history of a group can be represented as a phylogenetic tree, where the relationships among species (or genera, etc.) are shown in a diagram (similar to a genealogical tree) (Fig. 15.9)
One of the best sources of information about phylogenetic relationships are homologous structures (Fig. 13.3A)
Homologous structures are structures which derived from the same structure in a common ancestor
Example: our arm and a bat's wing, they both derived from a forelimb in a common ancestor, and then specialized differently later on
Analogous structures, on the other hand, can be highly misleading.
Analogous structures are morphologically very similar, because they have the same function, but they are NOT derived from the same structure in a common ancestor (Fig. 15.11)
Example: a bat's wing and a bee's wing; a shark's fin and a dolphin's or a penguin's fin
Today there are new and very powerful tools to study evolutionary relationships
AS YOU SHOULD KNOW..
The characteristics of an organism are ultimately determined by the nucleotide sequences in its DNA.
So, a comparison of the DNA (and proteins) from different organisms highlights the organisms' basic differences and similarities.
Nowadays amino acids sequencing, DNA and RNA sequencing are commonly used to establish evolutionary relationships among organisms (Figs. 15.12A and B)
Classification of life
Systematics is the study of biological diversity and classification
Taxonomy is the identification and classification of species
Phylogeny is the study of evolutionary relationships of species
The first step is assigning scientific names to species.
We still use the system proposed by the Swedish botanist Carolus Linnaeus in the 1700s.
This is a binomial system, i.e. two-names system to name each species. These two names are latinized.
The first part of the name is the genus (capitalized) to which the species belongs (example Canis)
The second part is the species (example familiaris = domestic dog; lupus= wolf)
A major objective of systematics is to group species into broader taxonomic categories, using a system also proposed by Linnaeus.
Beyond grouping the species within genera, it places similar genera in the same family, groups families into orders, orders into classes, classes into phyla and phyla into kingdoms (Fig. 15.10)
How many kingdoms?
Linnaeus proposed a two-kingdom scheme, where he divided all life in plants and animals.
His scheme was accepted for more than two centuries.
But where do you put the prokaryotes?
In 1969 Whittaker proposed a five-kingdom scheme, based on similarities and differences in cell structure, morphology, developmental features, and mode of nutrition (Fig. 15.14A)
Monera: prokaryotes
Fungi: multicelled eukaryotes, heterotrophs, decomposers
Plantae: multicelled producers
Animalia: multicelled heterotrophs
Protista: whatever does not fit in the other kingdoms!
Recently, another scheme has been proposed, with 3 kingdoms: all the eukaryotes are grouped in one kingdom (kingdom Eukarya), while the prokaryotes are divided in two groups, the Archaeobacteria (kingdom Archaea) and the Eubacteria (kingdom Bacteria). Archaea and Bacteria differ in many biochemical, structural etc. features. Archaea are more closely related to Eukarya than the Bacteria (Fig. 15.14B)
EXAMPLE OF TEST QUESTIONS
RESULTS OF TEST 3
Total students present: 248
7 A (2.8%)
24 B (9.6%)
35 C (14.1%)
64 D (25.7%)
119 F (47.8%)
TO CALCULATE YOUR GRADE: 2*(# of correct answers) + 4
Chapter 16. The Origin and evolution of microbial life: Prokaryotes and Protists
Life originated about 3.8 bya
How did it arise and in which physical and chemical conditions?
4 bya the Earth was a thin-crusted inferno. In less than 200 million years, life originated on his surface (Fig. 16.1A).
The universe was not always like now. It seems that once it was all compressed in one big mass. Some 10-20 billion years ago it exploded in what is called the "big bang" and it has expanded ever since.
Our solar system formed from a cloud of dust. Most dust condensed in the sun, but some matter was left orbiting around the baby-sun in concentric rings. Each ring gave rise to a planet.
Earth probably began 4.5 bya as a cold world, but later on, with impact of meteorites, tight compaction due by gravity etc. it became a molten mass. The less dense (= the lighter) material became concentrated on the surface and slowly solidified. The first atmosphere was probably composed of hot H2, which soon escaped from into space.
A new atmosphere soon was formed by volcanic activities. This second atmosphere probably consisted of CO, CO2, N2, H2O, CH4 and NH4
The first seas were formed by torrential rains when the planet cooled enough for the water vapor to condense. UV radiation and lightning were much more intense than today. Here life arose!! (Fig. 16.1A)
How did life originated?
The earliest form of life was much simpler than today's, and life developed from non-living material.
What's the primary attribute of life? Self-replication
So, the earliest lifelike entities were probably aggregates of simple molecules that could self-replicate
In 1953, S. Miller demonstrated that it is possible to obtain simple organic molecules from inorganic material. He simulated the early atmosphere, he put electrodes to spark it to mimic lightning and in less than a week he found amino acids and other organic molecules! (Figs. 16.3A and B)
After organic molecules formed in this lifeless world, the second big step would have been polymerization, i.e. formation of complex molecules (nucleic acids and proteins).
In the cell, polymerization is catalyzed by enzymes. But polymerization can take place if solution of organic monomers are dripped onto a hot surface (e.g. hot rock). In this way, the water vaporizes and the monomers concentrate and can spontaneously bind together.
Since the primary attribute of life is self-replication, and only nucleic acids are able to replicate themselves, probably the first genes were short strands of RNA which was able to replicate themselves on hot clay,without enzymes (Fig. 16.5)
This is called the RNA world
However, we are still far from a living cell.
Probably, before a cell appeared, some molecular cooperation started to take place.
Probably the first molecular cooperation involved translation of an RNA template into a protein, without the help of any enzyme. If then in turn the polypeptide behaved as an enzyme for RNA replication, the molecular cooperation between nucleic acids and polypeptides would have began (Fig. 16.6A)
If these cooperations started to become common, there might have been aquatic environments, especially small puddles, where high concentrations of large molecules were present.
It has been proven in the laboratory that in aqueous environments polypeptides can self-assemble in small spheres filled with liquid. If these microscopic spheres trapped some RNA and their peptide cooperators, it would have been the ancestor of the first cell! (Figs. 16.B and C)
KINGDOM MONERA
The fossil records shows that prokaryotes were abundant 3.5 bya. They evolved all alone for about 2 billion years and nowadays they are found in all kind of environments that can support life.
The structure of a bacterium

Small cells, with a cell wall encasing the plasma membrane. Some bacteria posses an external gelatinous layer called capsule. Many bacteria possess flagella, and others may posses shorter outgrowths called pili. If exposed to harsh conditions, some bacteria form thick-walled endospores around their DNA and small amount of cytoplasm (e.g. Bacillus anthracis) (Fig. 16.13C)
Types of bacteria
Gram-positive and gram-negative (if they do not or do possess an extra membrane outside the cell wall). Shape: cocci (spherical), bacilli (rod shape) or spirilli (twisted) (Figs. 16.9 A, B and C)
Reproduction in bacteria
by binary fission
some have conjugation
Eubacteria and Archaebacteria
The prokaryotes are classified in two different kingdoms, the Archaea and the Bacteria, which diverged very long time ago.
They are different in many ways, the Archaea showing features intermediate between Bacteria and Eukarya See box at page 325 of the textbook).
EUBACTERIA
More than 400 genera of prokaryotes are recognized and, by far, most are eubacteria. We can classify them according to their mode of nutrition (See box at page 326 of the textbook)
Photoautrophic eubacteria: cyanobacteria, they are aerobic and release O2 when photosynthesizing. Most live in pond and other freshwater habitats. They are among the most common photoautotrophs on Earth. Some can also fix N2 (Figs. 16.14A and B)
Photoheterotrophic eubacteria: purple and green nonsulfur bacteria. They use sunlight as source of energy, but use H2S and H2 as electron donor, instead of water. Common in organic soils, and sediments of aquatic habitats
Chemoautotrophic eubacteria: nitrifying, sulfur-oxidizing and iron-oxidizing bacteria. They use inorganic compounds as electron donors. They are important in the global cycling of nitrogen, sulfur and other nutrients.
Chemoheterotrophic bacteria: most bacteria. Many are decomposers. Most pathogenic bacteria fall in this category.
Weird bacteria:
Magnetotactic bacteria: they have a chain of magnetite particles that serves as a tiny compass. These bacteria swim toward the bottom of a body of water, where the O2 concentration is lower and therefore more suitable for their growth.
Myxobacteria: they form predatory colonies. This colony moves as a single organism and when conditions are favorable, the colony differentiate in fruiting bodies, spores are dispersed and each spore may give rise to a new colony.
Lyme disease and many other diseases are caused by bacteria (Figs. 16.15A and B, 16.6 A and B).
ARCHAEBACTERIA
The kingdom of Archaebacteria can be divided into 3 groups.
Methanogens: anaerobic bacteria, die in presence of O2. They live in swamps, sewage, animal guts and other oxygen-free habitats. They produce methane (2 billion tons per year). Their activity affect the levels of CO2 in the atmosphere.
Halophiles: live in brackish water, salt lakes, hydrothermal vents, and other high-salinity environments. Halophiles can spoil salted fish, animal hides and commercially produced sea salt (Fig. 16.12)
Extreme thermophiles: live in highly acidic soils, hot springs, coal mine wastes, hydrothermal vents.
EUKARYOTES
The fossil record suggests that eukaryotes evolved from prokaryotes about 1.7 mya. The main feature that differentiates a prokaryote from an eukaryote is the presence of membrane-bound organelles.
How did they evolve? Probably it happened in two steps.
The first step is membrane-infolding: endoplasmic reticulum (ER) and nuclear envelop derive from inward folds of a prokaryotic cell (Fig. 16.20A)
The second step is a very different process and is called endosymbiosis, and it is how mitochondria and chloroplasts evolved. Mitochondria and chloroplasts apparently evolved from small prokaryotes that took residence in a bigger prokaryote (the host) (Fig. 16.20B).
The ancestor of mitochondria might have been a small heterotrophic prokaryote able to use O2 to release energy (cellular respiration).
The ancestor of chloroplasts might have been a photosynthetic prokaryote.
Since almost all eukaryotes have mitochondria but only some have chloroplasts, it is believed that mitochondria evolved first
Another essential difference between prokaryotes and eukaryotes is the capacity for sexual reproduction among eukaryotes.
In sexual reproduction, two different parents contribute gametes to form the offspring. Sexual reproduction is not the only way eukaryotes can reproduce. At least some of them can also reproduce by asexual reproduction. In this way, the offspring are genetically identical to the parents, barring mutation. Most protists do not perform sexual reproduction unless they are under stress.
Why and how did sex arise?
Many protists form a diploid cell only if under stress. It seems to occurs because only in a diploid cell can certain kind of chromosome damage be repaired effectively.
The early stage of meiosis , where the 2 copies of each chromosome line up and pair with each other, seems to have evolved originally as a mechanism for repairing doublestrand damage to DNA by using the undamaged version of the chromosome as a template.
Thus it seems likely that sexual reproduction and the close association between pairs of chromosomes that occurs during meiosis first evolved as mechanisms to repair chromosomal damage
Why is sex important?
One of the most important evolutionary innovations of eukaryotes was the invention of sex.
Sexual reproduction provides a powerful mean of shuffling genes, quickly generating different combinations of genes among individuals.
The genetic recombination produced by sexual reproduction has had an enormous evolutionary impact because of its ability to rapidly generate extensive genetic diversity
Kinds of life cycles in sexually reproducing organisms
KINGDOM PROTISTA
Very diverse eukaryotes, mostly unicellular but also some multicellular. Probably the kingdom Protista will be split in several kingdoms in the future
The animal-like Protista: the Protozoans
About 65,000 species, they live in all aquatic environments. They can be free-living, either predators or decomposers, or parasites. Among the parasitic protozoans some cause major human diseases. There are 4 major groups of protozoans.
1) Amoeboid protozoans: naked amoebas, foraminiferans, radiolarians. All heterotrophs and do not have a permanent locomotor apparatus (Fig. 16.22B)
2) Animal-like flagellates: free-living or parasites, they bear one or more flagella. The free-living species live in freshwater or marine habitats. Parasitic types live in the moist tissues of plants and animals, including humans. Trypanosoma brucei causes African sleeping sickness, and it can damage the CNS; T. vaginalis is a parasite of the sexual apparatus and can damage also the urinary tracts. Giardia lamblia is an internal parasite that rarely is fatal. (Fig. 16.22A)
3) Ciliated protozoans: they have profuse arrays of cilia at their surface. They mostly use them to swim in freshwater or marine habitats, where they prey on bacteria, tiny algae, or other ciliates. Most of them are free-living and they are characterized by having two types of nuclei: a macronucleus and micronucleus. The micronucleus which undergoes meiosis and function in sexual reproduction (Fig. 16.22D)
4) Apicomplexa (or Sporozoans): all parasitic, some can cause serious diseases in humans. At one end of the body (apex) they have a complex of structures that function in penetrating the host cell. Plasmodium causes malaria; Cryptosporidium causes intestinal disorders (in 1993 thousands of people were hospitalized in Milwaukee); Toxoplasma causes toxoplasmosis, a disease that can cause birth defects. There are no effective vaccines against them (Fig. 16.22C)
Cellular slime molds: fungi-like protists
They have both unicellular and multicellular phases. They mainly live on rotting trees and other decaying matter. They are heterotrophs and predators. When food is abundant, they have a unicellular life stage. When food is scarce, many individual cells aggregate and form a slimy mass that moves in search of food. Later on, the mass forms a spore-bearing structure which release the spores (Fig. 16.23)
Photosynthetic protists I: unicellular algae
Many different kinds of organisms, photosynthetic with some exceptions. Focus on 3 groups.
1) Dinoflagellates: unicellular algae very common in freshwater and marine environments. Autotrophs or heterotrophs. They have two flagella. Different pigments give different colors. They can produce blooms known as red or brown tides. Some produce toxins (Fig. 16.25A)
2) Diatoms: unicellular, photosynthetic algae with a unique cell wall made of silica. The cell wall is made of two halves. They can live in both marine and freshwater habitats, and they count for over 40% of the total primary production in marine ecosystems. The shells of fossil diatoms form thick deposits known as diatomaceous earth. It is used commercially as an abrasive (Fig. 16.25B)
3) Unicellular green algae: photosynthetic, they most resemble plants both biochemically and structurally and may be their closest relatives. There are more than 7,000 species of green algae. Most live in freshwater (Fig. 16.25C)
MULTICELLULAR PROTISTS
Multicellular organisms probably evolved from colonial protists, whose cells became specialized and interdependent (Fig. 16.27)
It seems that this phenomenon did not happen only one time, but several, each one giving rise to a phylum.
Multicellular protists: macroalgae or seaweeds
Seaweeds are benthonic multicellular protists, all photosynthetic. They lack true tissue organization and therefore their body is called thallus. They live mostly in marine habitats, some are found in freshwater.
Divided in 3 major groups.
They have all the 3 kinds of life cycles
Brown algae: about 1,500 species, almost exclusively in marine water. They are closely related to diatoms. Some species (=kelp) can reach large sizes (over 40 mt long). Giant kelp have the body divided in stipe, blades and holdfast, but they are not considered real tissues (Fig. 16.26A)
Exploited for some chemical compounds in California (alginates, used to make toothpaste, yogurt, creamy desserts, ice cream, etc.) They can have all the 3 types of life cycle.
Red algae: > 5,000 species, almost exclusively in marine environment. They normally are fleshy but some species have the cell walls hardened by calcium carbonate: they are important in coral reef habitats as reef builders (Fig. 16.26B). They have a complex life cycle (alternation of generations). Some species are edible (nori: sushi), and others are used to extract agar and carrageenan, compounds used in cosmetics, food (jell-o, bakery, etc.) and in the lab (gel electrophoresis).
Green algae: the multicellular green algae are mostly marine; some species are fleshy (the sea lettuce) others, mostly tropical, have calcium carbonate in their cell walls, and are important as reef builders. They have sexual life cycle (all 3 types are represented) but can largely reproduce asexually (Fig. 16.26C). Ulva (the sea lettuce) lives in nutrient rich environments (polluted) and can can cause green tides. Some species are edible (Codium, Ulva)
Chapter 17. Plants, fungi and the colonization of land
KINGDOM FUNGI
Fungi are very peculiar organisms that evolved around 900 mya and colonized land around 440 mya; today there are around 100,000 species.
They are very different from plants and their main features are:
Fungi are heterotrophs; mostly they are decomposers but some are parasitic or active predators Fungi have filamentous bodies Their cell walls are made of chitin (like a crab shell) Unlike the other eukaryotes, they have nuclear mitosis (i.e. the nuclear envelope does not break down and reform. Instead mitosis takes place within the nucleus).
The body of a fungus
Fungi exist mainly in the form of slender filaments, called hyphae. A hypha is a long string of cells. The walls dividing one cell from another are called septa, but they are normally not complete -> cytoplasmic flow (Fig. 17.16D)
The network of hyphae is called mycelium, and it is the main body of the fungus (Fig. 17.16A). Fungi are unable to move to search for food. However they make up for the lack of mobility by a phenomenal growth rate.
All fungi obtain their food by secreting digestive enzymes in their surroundings and then absorbing back the resulting organic molecules -> external digestion
Many fungi are able to break down the cellulose in the wood, using it as food -> they are very important in recycling nutrients (Figs. 17.15C & 17.16B)
Other fungi are parasitic on plants or animals (Fig. 17.15A), while others are active predators. The edible oyster fungus attracts nematodes and secrets a substance that anesthetizes them. When the worms become inactive, the hyphae envelop and penetrate their bodies and absorb their contents (Fig. 17.15B)
Reproduction in fungi
Fungi can reproduce either asexually or sexually. All nuclei, except for the zygote, are haploid. The mycelia exist in two different mating types (+ and -) and only mycelia of different types can mate. When 2 mycelia (one + and one -) come in contact, their hyphae fuse but their nuclei do not. The result is a dikaryotic mycelium, where each cell contains 2 genetically different nuclei. This dikaryotic mycelium forms the fruiting body (mushroom) and in the cap specialized cells fuse and become zygotes by fusing their nuclei.
The zygote immediately undergoes meiosis and haploid spores are formed. Each one will germinate in a new haploid mycelium (Fig. 17.17)
Kinds of fungi
Fungi are divided in 4 groups:
Ascomycota (yeast, truffles, morels)
Basidiomycota (mushrooms, rusts) (Fig. 17.16C)
Zygomycota (black bread mold)
Imperfect fungi (Penicillium, Aspergillus)
Fungal associations
1) Lichens: these organisms are a symbiotic association between a fungus and a photosynthetic organism (cyanobacteria or green algae). The fungus is the largest part of the lichen. Both the fungus and the photosymbiont loose their cell wall and undergo cytoplasmic fusion (Figs. 17.18A & B). They are very resistant to drought and cold (Fig. 17.18C), and there are able to live in the harshest environments -> pioneer organisms. They are very sensitive to pollution (especially SO2) -> good environmental indicators.
2) Mycorrhizae: symbiotic associations between a fungus and the roots of a plant. The fungus benefits by absorbing carbohydrates from the plant, while the plant absorbs minerals from the fungus. They can be exomycorrhizae or endomycorrhizae (more common). 80% of all vascular plants form mycorrhizae (Fig. at page 345 of textbook).
Benefits from fungi
Nutrient cycling and forest health
Food: bakery, blue cheese and mushrooms (Fig. 17.20A)
Antibiotics (Fig. 17.20B)
Fungi as parasites or nuisance
Crop damage (fruit trees, cereals) and plant damage (Dutch elm disease) (Figs. 17.15A, 17.19A &B)
Toxic or poisonous fungi and mushrooms
Diseases: allergic reactions (Aspergillus); infections of mucous membranes (Candida) and skin (Epidermophyton); pneumonia (Pneumocystis); ergotism (Claviceps) (Fig. 17.19C)
KINGDOM PLANTAE
Plants are complex multicellular organisms that are terrestrial autotrophs, and evolved about 440 mya. Today, plants are the dominant organisms on the surface of earth. An estimated of 266,000 species are existing today.
Origin of plants
Plants and green algae show many similarities (biochemical, morphological, and structural features): they share the same photosynthetic pigments, the same type of chloroplasts, the same cell wall constituent, and cell division occurs in the same way.
Therefore, some green algae are possibly the ancestor of land plants. DNA analyses revealed that the closest relative to land plant is a freshwater green alga, Coleochaete, in the group of the Charophytes. (Fig. 17.2A)
Adaptations to terrestrial living
Green algae live in aquatic environment (Fig. 17.1A). To conquer land, they first had to overcome 3 environmental changes:
they had to absorb minerals from the rocky surface they had to find means of conserving water they had to develop a way to reproduce on land
1) Absorbing minerals: plants require large amounts of N, K, Ca, P, Mg and S. Each of these minerals constitutes 1% or more of a plant's dry weight. Algae absorb these minerals from the surrounding water, but where does a land plant get them? The first plants seem to have developed a special relationships with fungi that was a key factor in their ability to absorb minerals in terrestrial habitats. Within the roots of many early fossil plants can be seen fungi. This symbiotic association is called mycorrhizae (Fig. at page 345 of textbook)
2) Conserving water: one of the key challenges of living on land is to avoid drying out; to solve this problem, plants have a watertight outer covering called cuticle. The covering is formed from a waxy substance impermeable to water and cover the stem and the leaves. Water enters the plant only from the roots, while the cuticle prevents its loss to the air. Exchange do exist in the form of specialized pores called stomata. Water passes out through the stoma and CO2 enters it. The cells around the pore (called guard cells) expand and contract, controlling the loss of water while allowing the entrance of CO2 .
3) Reproduction on land: to reproduce sexually on land, it is necessary to pass gametes from one individual to another, and because plants cannot move around, it is necessary that the gametes avoid drying out while they are transferred by wind or insects. In the first plants, the eggs were surrounded by a jacket of cells, and a film of water was required for the sperm to swim to the egg and fertilize it. Today, mosses still reproduce this way. However, soon after mosses evolved, changes occurred in the plant life cycle that favored the development of spores, very resistant to dry out.
All plants have a life cycle involving alternation of generations (Fig. 17.4)
POP QUIZ solution:
1) Kingdom Protista, diatom
2) Kingdom Protista, dinoflagellate
3) Kingdom Protista, unicellular green alga
4) Kingdom Monera, cyanobacteria (photosynthetic bacteria)
Evolution of vascular system
Once plants became established on land, many other features developed gradually that aided their evolutionary success in this new habitat.
One of the most important structural changes in the gradual adaptation of plants involved better ways of moving water around the body of the plant. In order for a plant to grow high into the air, a relatively efficient plumbing system is required to carry water up from the roots to the leaves and to carry carbohydrates down from the leaves to the roots. This system is the vascular system (FIG. 17.1B). Of 12 phyla of living plants, 9 are vascular. The first vascular plants' fossils appeared around 410 mya.
1) Plants with no vascular systems: liverworts and hornworts
The first successful land plants had no vascular system. This greatly limited the maximum size of the plant body because all materials had to be transported by osmosis and diffusion. Only two groups of living plants, the liverworts and the hornworts lack a vascular system. They usually live inconspicuously in moist and shady places
2) Plants with simple vascular system: mosses
Mosses were the first land plants to evolve strands of specialized cell that conduct water and carbohydrates, so called vascular tissue. The moss vascular system is composed of conducting cells without specialized wall thickenings, like soft pipes, they cannot carry the water very high (FIG. 17.3B)
Liverworts, hornworts and mosses are called Bryophyta. They have a life cycle where the haploid gametophyte is the dominant generation (Fig. 17.5).
Mosses are very sensitive to air pollution -> environmental indicators.
Sphagnum, a peat moss, is one of the few mosses that can grow fast. It is harvested and dried to be burned and generate electricity in power plants. Compared with coal burning, peat fires generate fewer pollutants.
Vascular system
Sieve elements are relatively soft-walled cells that conduct carbohydrates away from the areas where they are made. They form the tissue called phloem.
Tracheary elements are hard-walled cells (which are dead) that transport water and dissolved minerals up from the root. They form the tissue called xylem.
see fig. 17.1B
Vascular plants
Majority of today's land plants (>250,000 species). Vascular plants appeared around 430 mya, with the first complete fossil dated 410 mya.
They are distinguished by several features:
Dominant sporophyte Specialized conducting tissue: water- and nutrient-conducting cells have reinforced cell walls to withstand considerable hydrostatic pressure Specialized body form: it is among vascular plants that we first see the traditional plant architecture of roots, stems and leaves
3) Seedless vascular plants: ferns, fern-like and club mosses
They differ from the Bryophytes in three key aspects:
The sporophyte is not dependent from the gametophyte The sporophyte has true vascular system The sporophyte is the longer phase of the life cycle
Most seedless vascular plants live in moist habitats and their gametophytes lack vascular tissues. Water droplets clinging to the plants are the only means by which flagellated sperms can reach the eggs. The few species living in dry habitats reproduce sexually during seasonal pulses of heavy rains (Fig. 17.3C).
Life cycle of ferns: see Fig. 17.6
300 mya, during the Carboniferous, mild climates prevailed and swamps flourished. Seedless trees were able to grow up to 40 mt high. Sea levels rose and fell 50 times during the Carboniferous. Each time the sea receded, the swamp forests flourished. When the seas moved back in, forest trees became submerged and buried in sediments. With time, these compressed organic remains were transformed into coal (Fig. 17.7)
The advent of seeds
A seed is a plant embryo with a durable, watertight cover. The seed is a crucial adaptation to life on land because it protects the embryonic plant from drying out when it is at its most vulnerable stage.
4) Gymnosperms: plants with "naked" seeds
Today's most widespread gymnosperms are the conifers. The seeds (ovules) of conifers develop on scales within the cones and are exposed at the time of pollination. Most conifers are adapted to live in moderately dry regions (Figs. 17.9A &C)
Life cycle of a conifer: see Fig. 17.8
In all seed plants, the gametophyte generation is greatly reduced and totally dependent from the sporophyte
5) Angiosperms: the flowering, seed-bearing plants
Angiosperms, in which the ovum is COMPLETELY enclosed by sporophyte tissue when it is fertilized, are today's most successful plants, 80-90% of all living plants. Virtually all our food is derived, directly or indirectly, from angiosperms.
The flower is the centerpiece of angiosperm evolution (Figs. 17.11A &B)
Life cycle of an angiosperm: see Fig. 17.12
The main difference between gymnosperm and angiosperm life cycle is that the seeds of the angiosperms are protected by the sporophyte tissue, i.e. the fruit, which is the thickened wall of the ovary
Why are angiosperms so successful?
More efficient leaves for photosynthesis Shorter life cycle than gymnosperms Protection of the seed Animal- plant interactions, both for pollination and seed dispersal (Figs. 17.13A, B &C; Figs. 17.14 A, B &C)
Chapter 18. The evolution of animal diversity
KINGDOM ANIMALIA
The key features of animals are:
Multicellular organisms, almost all diploids Heterotrophs, either predators or parasites Most animals are motile during at least part of the life cycle Their cells lack a cell wall Peculiar embryonic development
Embryonic development (Fig. 18.1)
The zygote develops in a stage called blastula. The blastula consists of a single layer of cells surrounding a hollow cavity.
Later, one side of the blastula folds inward, forming the gastrula.
The gastrula develops into a sack-like embryo with an opening at one end. At this point, the gastrula has an outer cell layer (the ectoderm) and an inner cell layer (the endoderm) that results from infolding. In most animals, a third layer (the mesoderm) forms between the other two. Each cell layer will develop in determined tissues and organs.
Animals probably originated from colonial protists
Animals probably evolved from heterotroph colonial protists, by cell differentiation and specialization. Later on, one side of the colony may have folded inward, providing a temporary digestive cavity. Eventually, the hollow cavity would have been filled and junctions holding the cells together would have developed (Fig. 18.2).
The simplest animals: sponges, animals without tissues
All aquatic animals, most marine but few are freshwater. Their bodies contain a variety of highly specialized cells, although their cells are not organized into tissues. Most sponges completely lack symmetry.
The body of sponge is anchored on the seafloor and functions as a water-filtering machine. It is normally shaped as a vase, and perforated with tiny holes from where the water comes in. The outside of the body is covered with a skin of flattened epithelial cells that protect the sponge. A middle layer is composed of motile cells called amaebocytes and skeletal components (spicules).
In the third layer, facing the internal cavity, there are flagellated cells called choanocytes; the beating of their flagella drives the water from the pores into the cavity. In this way, the water is sent down through its collar, where food particles are trapped and ingested (Fig. 18.3C)
Sponges can reproduce both asexually and sexually, but they lack a gastrula stage of development. They probably evolved from colonial protists called choanoflagellates, which are very similar to the choanocytes of a sponge (Fig. 18.3D).
Cnidaria
Hydras, jellyfish, sea anemones, corals and comb jelly constitute the phylum Cnidaria (Figs. 18.4A, B & C). Most of them live in marine waters, few in freshwater.
They have radial symmetry and true tissues.
Body plans
The Cnidaria show two different body form, the medusa and the polyp. Both have a sac-like gut. Medusae float; some look like bells. The mouth, centered under the bell, may have extensions to assist in prey capture and feeding (Fig. 18.4B). Polyps have a tube-like body with a tentacle-fringed mouth at one end. Usually the other end is attached to the substrate (Fig. 18.4C)
Cnidaria have an external epidermis, a middle gelatinous layer called mesoglea, and an inner layer called gastrodermis. Embedded in these layers there are nerve cells and contractile cells. The mouth leads to a digestive compartment called gastrovascular cavity, where digestion takes place. Unlike sponges, cnidarians have extracellular digestion, i.e. food is digested outside the cell, in the gut cavity
Exclusive to this phylum are cnidocytes, unique stinging cell. Within each cnidocyte there is a small harpoon called nematocyst, used by the animal to capture their prey. The cnydocyte builds up a very high internal osmotic pressure and uses it to push the nematocyst outward (Fig. 18.4D).
The advent of bilateral symmetry
All other animals (besides Echinoderms) have bilateral instead of radial symmetry.
Bilateral symmetry was a major evolutionary advance because it allows different part of the body to become specialized in different ways. For example, most bilaterally symmetrical animals have evolved a definite head end, a process called cephalization (Fig. 18.5).
Animals with head are often active and mobile, moving through their environment headfirst, with sensory organs concentrated in front so the animal can test for food, danger and mates
The simplest bilateral animals: flatworms
Flatworms (phylum Platyhelminthes) are the simplest bilateral animals (Fig. 18.6A)
They have internal organs (organ: association of one or more kinds of tissues that function as a unit).
Flat worms lack any internal cavity other than the digestive tract. The gut is completely surrounded by tissues and organs. They are called acoelomates, i.e. without a body cavity (Fig. 18.7A)
Flatworms are thin because of their acoelomate body design. They lack any circulatory system, so dissolved O2, CO2 and nutrients must pass through the solid body by diffusion. Having a thin body helps a lot. The gut is highly branched to help diffusion and has only one opening (no anus). They can reproduce asexually, by fission, or sexually (mostly they are hermaphrodytes).
Parasitic flatworms
Tapeworms and flukes are parasitic (Fig. 18.6C). Schistosoma japonicum penetrates in the human body through the skin and goes in intestinal veins. White blood cells attack them and grainy masses form in tissues. In time, liver, spleen, bladder and kidneys deteriorate. About 200 million people are infected, mainly in SE Asia (Fig. 18.6B).
The advent of a body cavity
The evolution of a body cavity, i.e. a fluid-filled space between the digestive tract and the body wall, was an important improvement in animal body design for several reasons:
Circulation: fluids that move within the body cavity can serve the function of a circulatory system, opening the way to larger bodies. Movement: fluid in the cavity makes the animal's body rigid, permitting resistance to muscle contraction and thus opening the way to muscle-driven body movement. Organ function: in a fluid-filled enclosure, body organs can function without being deformed by surrounding muscles. For example, food can pass through a gut suspended in a cavity freely, at a rate not controlled by when the animal moves.
Coelom and pseudocoelom (Fig. 18.7C)
A pseudocoelom is an internal space in direct contact with the wall of the digestive tract. The outer edge of the pseudocoelom contacts a muscle layer that is part of the body wall.
A true coelom is a body cavity that is completely lined by a middle tissue layer. This tissue layer extends from the body wall and wraps around the digestive tract. The middle layer suspends the digestive tract and other internal organs from the body wall.
Pseudocoelomates: roundworms
Roundworms (phylum Nematoda) are an example of pseudocoelomate organisms (Figs. 18.7B & 18.8A). They are mostly microscopic worms with a tough outer covering, the cuticle, very resistant to dryness and crushing. Roundworms have also a complete digestive tract, with a mouth and an anus. Between the gut and the body wall is a false coelom. The cells in all tissues absorb nutrients from coelomic fluid and give up wastes to it.
Parasitic nematodes (Fig. 18.8B)
Most nematodes are parasitic, and they can do extensive damage to their hosts, which includes humans, cats, dogs, cows, sheep as well as soybean, potatoes and other crop plants. They are all thin but they can grow long: some in female sperm whales are nine meters long!
Elephantiasis is caused by roundworms (Wuchereria): adult worms become lodged in the lymph nodes and can obstruct the flow of lymph. This causes fluid to back up and accumulate in tissues. A mosquito is its intermediate host.
Mollusca
Mollusca are the second largest animal phylum, with > 110,000 species. They occur almost everywhere, and they are the second most successful land animals (35,000 species).
They have a true coelom, i.e. body cavity entirely enclosed within the mesoderm. This allows development of highly specialized organs (e.g. stomach).
Mollusca includes 3 classes, with different body plans.
All mollusks have three different body parts: a head, a central section with the body's organs and a foot. The foot is a muscular portion of the body used for locomotion.All around the body there is a heavy fold of tissue called the mantle, unique feature of mollusks. The mantle has many functions, such as producing the shell, housing the gills, etc.They also have a circulatory system, an organ system that distributes nutrients and water throughout the body. Some mollusks have a organ called radula, used to scrap algae off rocks. Others (like octopuses) use it as a weapon to puncture their prey (Fig. 18.9A)
Gastropods (snails and slugs): about 90,000 species, they live in all environments, use the foot to crawl. Their mantle often, but not always, secretes a single hard protective shell. All terrestrial mollusks are gastropods (Figs. 18.9B &C)
Bivalves (clams, oysters and scallops): their mantle secretes a two-part shell with a hinge. They filter-feed by drawing water into the shell. Humans have been eating one type of bivalve or another since prehistoric times (Fig. 18.9D)
Cephalopods (octopuses and squids): they are highly active predators of the seas. They includes the swiftest invertebrates (jet-propelled squids), the largest of all known invertebrates (giant squid) and the smartest (octopuses). They have modified the mantle cavity to create a jet propulsion system that can propel them rapidly through the water. Their shell is greatly reduced to an internal structure or is absent (Figs. 18.9E & F)
The advent of segmentation
Another major body feature in evolution is body segmentation, i.e. the subdivision of the body along its length into a series of repeated parts (segments) (Figs. 18.10A, B & C)
A segmented body is advantageous in many ways: it allows great body flexibility and mobility and it probably evolved as an adaptation for movement
Segmented worms: Anellida
About 15,000 species, 2/3 live in the sea, the others in freshwater (most leeches) or moist soil (earthworms) (Figs. 18.11A, B & C).
Their body is divided in segments, each of them with a coelomic chamber. In most chambers we find repeats of muscles, blood vessels, branching nerves and other organs. The gut extends through all the chambers, from mouth to anus. They have a cuticle of secreted material that surrounds the body surface. It bends easily and is permeable to water and gases. The fluid-cushioned coelomic chambers serve as a hydrostatic skeleton against which the muscles act.
Arthropods: the most successful organisms on Earth
Evolutionarily speaking, "success" means having the greatest number of species, producing the most offspring, occupying the most habitats, effectively fending off predators and competitors and having a capacity to exploit the greatest amounts and kinds of food. Over a million different species are known to belong to the phylum Arthropoda.
Arthropods include crustaceans, insects, arachnida (spiders, scorpions), millipedes and centipedes.
Six adaptations of arthropods that contributed to their success
A hardened exoskeleton: external skeleton mainly made of chitin. It probably evolved as defenses against predation, but then took on other functions on land (avoids water loss, supports the body). To grow in this hard shell, arthropods molt repeatedly during their life Jointed appendages: arthropods' appendages have thin cuticle at joints, where associated muscles can bend the cuticle and allow movement Fused and modified segments: segments of the body are fused together and modified for very specialized functions Specialized respiratory structures: very specialized structures (lungs in land arthropods) to support energy-consuming activities Efficient nervous system and sensory organs: intricate eyes and other sensory organs are very specialized Division of labor in the life cycle: most arthropods undergo metamorphosis. Typically, immature stages such as caterpillars specialize in feeding and growing in size, and the adult specializes mainly in dispersal and reproduction
Spiders and the other arachnids
They do not have mandibles. Their segments are fused in a forebody and a hindbody. The forebody appendages include four pairs of legs, a pair of sensory appendages and a pair of appendages used for predation. Most arachnids are predators. Some are poisonous or can cause serious diseases (Lyme disease). Ticks are parasites (blood-sucking) (Figs. 18.12C)
Crustaceans
Most crustaceans live in marine waters, but some are also in freshwater and terrestrial habitats. The simplest crustaceans have many pairs of similar appendages for most of their length and may resemble their annelid ancestors. In others, the appendages evolve into diverse structures with different functions (Fig. 18.12A)
Most crustaceans are tiny and are part of the plankton; they feed on phytoplankton and are the main food source for baleen whales and many fish. Some are parasitic of fish and other aquatic organisms
Of all the arthropods, only barnacles have a calcified "shell", a modified external skeleton that protects them from predators, drying out and surf. Some of them attach themselves only to the skin of whales (Fig. 18.12D)
How many legs? Millipedes and centipedes
Millipedes have a rounded, segmented body. As they develop, pairs of segments fuse, so what looks like a single segment in the adult has two pairs of legs. They mostly are scavengers on decaying vegetation. Most millipedes have about 100 legs (Fig. 18.12E).
Centipedes have a flattened body, and all but two segments have a pair of walking legs. All species are fast-moving, aggressive predators with fangs and venom glands. The house centipede often lurks in buildings, where it actively preys on cockroaches, flies and other pests. Most have between 15 and 177 pairs of legs
Insects or the dominators of the Earth
There are about a million species known, and maybe as much as 2 millions yet to be discovered. They are the most abundant eukaryotes on earth. They primarily live on land, but some have colonized freshwater habitats and few also marine habitats. About 70% of all the named animal species are insects.
Most insect are relatively small, ranging from 0.1 mm to about 30 cm in length (Figs. 18.13B-G)
Insects have 3 body regions (Fig. 18.13A):
1) Head: the head of insects is very elaborate, with a single pair of antennae and elaborate mouthparts. Most insects have compound eyes, which are composed of independent visual units.
2) Thorax: the thorax consists of 3 segments, each of which has a pair of legs (= 6 legs). Most insects also have two pairs of wings attached to the thorax. In some insects like flies, one of the pair of wings has been lost during the course of evolution
3) Abdomen: the abdomen consists of up to 12 segments. Digestion takes place primarily in the stomach and excretion takes places through organs called Malpighian tubules. These organs were a key adaptation facilitating invasion of the land by arthropods
Insects have a variety of diets: the mouthparts are modified according to the dietary habits of the species.
Examples:
Mosquito's mouthparts are adapted to pierce skin and suck blood; Butterflies' mouthparts are adapted to suck nectar from flowers Housefly's mouthparts are adapted to sop up liquids
Echinoderms: the puzzling evolutionary branch
Echinoderms (sea stars, sea urchins, brittle stars, sea cucumbers and feather stars) evolved more than 650 mya (Figs. 18.14B &C).
They are, with the chordates, are called deuterostomes. They have a very different embryonic development from all the other animals we saw so far.
Echinoderms are all marine. They lack body segments and most are radially symmetrical as adults. The larval stage of echinoderms however, is bilaterally symmetrical.
Echinoderms have an endoskeleton, i.e. an internal skeleton composed of hard plates just beneath the skin. Adult echinoderms have a five-part body plan. Its nervous system consists of a central ring of nerves from which five branches arise. There is no centralization, i.e. no "brain".
Peculiar to these organisms is a water vascular system, a network of water-filled canals that branch into extensions called tube feet. At the base of each tube foot is a fluid-filled sac that act as a valve. When a sac contracts, its fluid is forced into the tube foot, extending it. When extended, the tube foot attaches itself to the ocean bottom. The sea star pulls against these tube feet and haul itself over the seafloor (Fig. 18.14A & B).
POP QUIZ solutions:
1) Kingdom Animalia, Class Reptilia (Archaeopteryx)
2) Kingdom Fungi, oyster tree or tree mushroom (Basidiomycota)
3) Kingdom Fungi, leafy lichen
4) Kingdom Fungi, lichen
5) Kingdom Animalia, sponge (Phylum Porifera)
6) Kingdom Animalia, organ pipe coral (Phylum Cnidaria)
Chordates
The Chordates have 4 distinguishing features:
A dorsal, hollow nerve cord A notocord, i.e. a flexible rod between the digestive tract and the nerve cord Gill structures in the pharinx A post-anal tail
Invertebrate chordates
There are 2 phyla of invertebrate chordates: tunicates and lancelets.
Tunicates
2,000 species, all marine. The larva is bilateral and resemble a tadpole. The adult are sac-like organisms, and secrete a gelatinous "tunic" around themselves. They live attached to the substrate, either solitarily or in colonies (Fig. 18.15A). They are filter-feeders.
The larva uses the notochord for fishlike swimming movements.
Lancelets
About 25 species, all marine. Like tunicate larvae, lancelets use the notochord to produce swimming motion. They are filter-feeder and live buried in sand and sediments. Their respiration mode is diffusion (Fig. 18.15B)
VERTEBRATES
The characteristics features of these organisms (which are the largest group of chordates) are:
A backbone composed of segmented units called vertebrae A skull
These skeletal elements enclose the main parts of the nervous system (Fig. 18.16). The first evolutionary step was a shift from the notochord to a hard backbone, where muscles could work against. A vertebral column evolved in fast-moving predators, some of which were ancestral to all other vertebrates.
First vertebrates: Agnathans or jawless fishes
Hagfishes and lampreys are the only living agnathans. About 75 species, with a cylindrical body, a cartilagineous skeleton and no paired fins.
Hagfish are predators, live in marine waters, where they prey on polychaete worms (Anellida) or look for weak or dead organisms. They defend themselves secreting sticky smelly mucus.
Lampreys are specialized predators that are almost parasites. Their suckerlike oral disk has horny, toothlike parts that rasp flesh from prey (Fig. 18.17A). Just before the turn of century, lampreys began invading the Great Lakes of N. America. Their introduction resulted in the collapse of populations of lake trouts and other large, valuable fishes.
Evolution of jaws
Jaws evolved through modification of structural elements that supported the gill slits (Fig. 18.17B). Jaws meant new feeding possibilities and greater competition among predators. The evolution of jaws allowed the evolution of a complex brain ( by expansion of part of the nerve cord)
Evolution of fins and gills
Other two important steps in the evolution of vertebrates are the the appearance of paired fins and gills.
Fins are appendages that help propel, stabilize and guide the body in the water. In some lineages, ventral fins became fleshy and equipped with skeletal supports. Paired, fleshy fins were the starting point for the legs, arms and wings that evolved among amphibians, reptiles, birds and mammals.
Gills are respiratory organs with moist, thin and much-folded surface, they are richly endowed with blood vessels and they offer a large surface area for gas exchange. Gills can't work out of the water: they stick together unless water flows through them and keep them moist. In the ancestor of land vertebrates, pouches developed from the gut wall. The pouches evolved into lungs, i.e. internally moistened sacs for gas exchange
JAWED FISHES
1) Cartilaginous fishes: sharks, rays, chimaeras. About 850 species, almost all marine predators (Fig. 18.18A). They have pronounced fins, a skeleton of cartilage and 5 to 7 gill slits on both side of the pharynx. Their body is covered with hard scales. Rays and skates are mainly bottom dwellers with flattened teeth suitable for crushing hard-shelled prey. They have enlarged fins that extend onto the side of the head. Some have venom glands or electric organs. Sharks are formidable predators, with sharp, triangular teeth that are continually shed and replaced.
2) Bony fishes: they are the most numerous and diverse vertebrates (about 21,000 species). Body plans vary greatly, but all bony fishes have a stiff skeleton reinforced by calcium salts, an operculum, i.e. a protective cover that protects the gill chamber; movement of the operculum allows the fish to breathe without swimming; they also have a swim bladder, a gas-filled sac to help maintain buoyancy (Figs. 18.18B & C).
All living bony fishes are ray-finned fishes, i.e. their fins are supported by thin, flexible skeletal rays.
Only seven living bony fishes (all the other are extinct) are lobe-finned, i.e. muscular fins supported by stout bones: the Latimeria chalumnae and 6 species of lungfishes (Fig. 18.18C)
Evolution of land vertebrates
The Coelacanth (lobe-finned fish) is a living fossil, relics of the first vertebrates that conquered land. Land vertebrates evolved during Devonian times, when the sea level swung up and down.
Ancestors of lobe-finned fish probably used their lobed fins to pull themselves from dried-up ponds to ones that were still habitable (Fig. 18.19C)
They had sac-shaped outpouchings from the wall of the esophagous, and started to use for gas exchange (living lungfishes live in stagnant water but surface to gulp air). The act of traveling out of water favored the evolution of stronger fins and more efficient lungs
Amphibia
Amphibians are the first land vertebrates. To successfully invade land, few major innovations needed to evolve:
Legs Lungs More efficient heart Reproduction in the water to prevent the eggs from drying out Protect the body from water loss
Amphibians solved these problems imperfectly, but well enough for them. They were the dominant land vertebrates for 100 my. They reached their greatest diversity during mid Permian period, and 60% of them were fully terrestrial; after the greatest mass extinction at the end of Permian they started to decline. Today, only 2 groups survive, both aquatic: the anurans (frogs and toads) and the urodeles (salamanders).
All of today's amphibians (about 4,200 species) must reproduce in water and live part of their lives there, so they are not completely terrestrial (Fig. 18.19B). Even when gills or lungs are present, amphibians can use their skin as a respiratory surface, and therefore must be kept moist.
Salamanders: carnivorous, both as larvae and as adults. The movement they do when walking resembles the fish movement when swimming. Some salamanders are paedomorphic (Fig. 15.7A)
Frogs and toads: > 3,000 species. Their long hindlimbs allow them to catapult in the air or barrel through the water. Some are poisonous (Fig. 18.19A).
Reptilia: the truly terrestrial vertebrates
Reptiles improved on the innovations first attempted by amphibians:
1) Legs were arranged to better support the body, allowing reptiles to be bigger and to run
2 & 3) Lungs and hearth were altered to be far more efficient
4) Eggs were encased in watertight covers
5) The skin was covered with dry scales to retain water
Today some 6,000 species of reptiles are found almost everywhere (Fig. 18.20a & B). When reptiles first evolved, about 320 mya, the world was entering a long, dry period, condition to which reptiles were very well suited, and thus quickly diversified. Their ability to retain water allowed them to have large bodies in dry conditions, while amphibians could not.Within 100 my, the large-body niche was totally taken over by reptiles, i.e. all land vertebrates bigger than a chicken-sized animal were reptiles (Fig. 18.20C).
Reptiles can lay eggs on land, unlike amphibians (Fig. 18.20A). Inside each egg, the embryo develops within a fluid-filled sac, the amnion. The embryo is nourished by yolk until hatches as a juvenile, ready to move about freely and feed itself. The evolution of this drought-resistant amniotic egg enabled reptiles to complete their life cycle on land.
They do not use their metabolism to control body temperature, and therefore they are called cold-blooded animals
Birds: the masters of air
Birds evolved from small bipedal dinosaurs about 150 mya, but they were not common until the dinosaurs became extinct. Birds are structurally so similar to reptiles that are considered an evolutionary branch of it.
The oldest bird of which we have fossil is the Archaeopteryx, which had feathers but shared many reptilian characters (teeth, long reptilian tail, etc.) (Fig. 18.21A).
Almost all the body of a bird is adapted for flight:
1) feathers, derived from reptilian scales (skin) are the ideal adaptation for flight because they are light and easily replaced
2) The skeleton is very light because, at least partially, the bones are hollow and contain air sacs.
3) A bird's flight muscles are very developed and attach to an enlarged breastbone, or sternum, and to upper limb bones adjacent to it
4) Circulatory and respiratory organs are extremely efficient to support flight
5) Birds are warm-blooded
The rise of mammals
Mammals evolved about 220 mya side by side with the dinosaurs
The key features of mammals are:
The female has mammary glands that produce milk to nurse the rapidly growing newborns Among all living vertebrates, only mammals have hair, and all mammals do. A hair is a filament composed of dead cells filled with the protein keratin. The primary function of hair is insulation
Like birds, mammals are warm-blooded. Today, there are three major groups of mammals:
1) Monotremes : the first mammals probably most closely resembled today's monotremes, which have a pelvic structure similar to early reptiles and lay shelled eggs. When the dinosaurs disappeared, their niche as large land vertebrates was taken over by such mammals, whose fur-insulated bodies were better suited to the colder climates that became typical then. Only 3 species are present today (Fig. 18.22A)
All the other mammals are born rather than hatched. The embryo is nurtured by an organ called the placenta, consisting of both embryonic and maternal tissue. The placenta joins the embryo to the mother within the mother's uterus.
2) Marsupials: they have a brief gestation and give birth to tiny, embryonic offspring that complete development while attached to nipples on the abdomen of the mother. The nursing young are housed in an external pouch (marsupium). Almost all marsupials live in Australia, New Zealand and Central and South America (Fig. 18.22B).
3) Eutherians: their placentas provide more intimate and long-lasting association between the mother and her developing young than do marsupial placentas. They are 95% of all mammal species (Fig. 18.22C).
Chapter 19. Human evolution
In 1871, C. Darwin published another book, "The descent of man". He suggested that humans evolved from the same African ape ancestor that gave rise to the gorilla and the chimpanzee.
As Darwin suspected, his idea was not very well taken by people.
In the US in the 1920s several states passed laws to make illegal to teach Darwin's theory of evolution in schools.
Even today, over 20 states permit schools to include creationism as an alternative to evolution in biology courses (!!!), although laws requiring "equal time" were ruled unconstitutional in 1986.
Primates
Probably the ancestor of primates (living about 80 mya) was a tree shrew. After dinosaurs went extinct, these animals begun to diversify, giving rise to the Primates.
Primates have two distinct evolutionary features:
Grasping fingers and toes Binocular vision: the eyes are in front rather than lateral, producing binocular vision that lets the brain judge distance precisely
Earliest Primates: prosimians (lemurs, lorises, tarsiers etc.) (Figs. 19.1A & B)
Today very few prosimians survive; most of them are nocturnal, with large eyes, and grasping hands. They are all endangered
Monkeys
The other group of Primates is the anthropoids (monkeys, apes and humans). They have a larger brain relative to body size and rely more on eyesight and less on the sense of smell. They are day active and have color vision.
Monkeys live in social groups and care for their young for a long period. They live in tropical habitats in Africa, Asia and Americas (Figs. 19.1C & D).
Apes
Apes are closely related to humans, and are bigger than any monkey, have a larger brain and their forelimbs are longer than their hindlimbs. They are all confined to tropical areas in Southeast Asia and Africa (Figs. 19.2A, B, C & D)
The evolution towards humans
By 5 million years ago, climate started to cool down. The vast tropical forests gave way to dry woodlands and grasslands. Food was harder to find, and it is in this changing environment that humans evolved.
Two critical steps were crucial to the evolution of humans:
Bipedalism: (short arms, bowl-shaped pelvis and spinal cord exiting from the bottom of the skull at a 90 degree angle) Larger brains Varied diet (omnivors instead of carnivors): different teeth for all occasions
The first hominid fossil of the genus Australopithecus was discovered in 1924 by R. Dart in S. Africa (2.8 my old). He called it A. africanus
In 1938 a second species, with massive teeth and jaws (A. robustus) was unearthed in S. Africa
In 1959 Mary Leakey discovered the "nutcracker man" (A. boisei) with very powerful jaws.
In 1974, D. Johanson found in Ethiopia the most complete and best preserved prehuman hominid ever, A. afarensis (Lucy) over 3 my old. She was a female and was bipedal, but the brain was no larger than an ape's. Apparently, hominids walked upright before they acquired large brains
The first humans
We are the third and only surviving species of humans.
The first humans, members of the genus Homo, evolved from australopithecine ancestors about 2 mya, only to be replaced by a second "improved version" of human that moved out of Africa and spread across the earth.
In the 1960s in Africa many remains of human fossils were found in Tanzania. The skulls (1.8 my old) had human characteristics rather than australopithecine. Because of its association with tools, it was called Homo habilis (handy man). He was small in stature.
After the publication of Darwin's book there was much discussion about the missing link, the fossil ancestor common to both humans and apes.
E. Dubois , trying to solve this, decided to seek fossil evidence of the missing link in the home country of the orangutan, Java.
In 1891 he found the Java man, which was:
an excellent walker with long straight legs he had a very large brain the bones seemed to be 500,000 years old
The fossil hominid that Dubois discovered was far older than any other fossil discovered up to that time, so scientists did not believe it was an ancient species of human. Finally, after years of hopeless arguing, Dubois in disgust buried the Java man under the floorboards of his dining room and refused to show it to anybody for 30 years!!
In the 1920s, near Beijing (China) another fossil was found, and it closely resembled the Java man. Crude tools were also found, and most important of all, the ashes of campfires. These findings (Java man and Peking man) are now recognized as belonging to the same species, Homo erectus. H. erectus was a lot larger than H. habilis (about 1.5 m tall). He had a rounded jaw and, most interestingly, he was able to talk.
In Africa was found a fossil of H. erectus, 1.5 my old (1 my older than the other two specimens), and its appearance marked the beginning of the great human expansion. Far more successful than H. abilis, H. erectus quickly became widespread and abundant in Africa, and within 1 million years had migrated into Asia and Europe.He was social, living in tribes of 20-50 people, often dwelling in caves. They hunted large animals and cooked them over fires.H. erectus survived for over a million years, longer than any other human species (in Africa, until 0.5 mya, in Asia until about 250,000 ya)
Our own species
Homo sapiens appeared in Africa between 500,000 and 300,000 ya.
The origin of human races is a much-debated point among scientists. Many have argued that the different races evolved from H. erectus independently, each adapted to a different place.
DNA analysis more recently has shown that all human races evolved from an ancestor in Africa, and he spread all over from there.
Neanderthal man
H. sapiens first appeared in Europe about 130,000 ya (Neanderthals).
Neanderthals were powerfully built, short and stocky. Their skulls were massive and their brain were very large. They made tools and lived in caves. They became very common by 70,000 ya. They buried their dead and believed in a life after death. This is the first time we have evidence of symbolic thinking.
Cro-Magnon man
Neanderthal abruptly disappeared about 34,000 ya and was replaced by an essentially modern human, the Cro-Magnon. They also came from Africa, spread in the middle east and then colonized Europe. They used sophisticated tools, lived in complex society and had full language capabilities. They lived by hunting.
Humans of modern appearance eventually spread across Siberia to N. America at least 13,000 ya.
EXAMPLE OF TEST QUESTIONS