22.

1 The Rise of Evolutionary Thought

● Contrast typological thinking, Lamarckian evolution, and Darwinian evolution.
● Describe Plato's typological thinking.
● Describe Aristotle's scale of nature.
● Describe Lamarckian evolution.
● Describe Darwin and Wallace’s theory of natural selection.

A. Plato and Typological Thinking

1. Plato saw species as unchanging, perfect “types” created by God. (Fig. 22.1a)
2. Plato thought individual variation was an unimportant deviation from the true “type.”

B. Aristotle and the Scale of Nature

1. Aristotle, like Plato, thought species were unchanging types.
2. Aristotle thought species could be organized into a sequence or ladder of increasing complexity,
with humans at the top. (Fig. 22.1b)

C. Lamarck and the Idea of Evolution as Change through Time

1. Lamarck noticed that organisms changed over time.
2. Lamarck thought animals progressed over time from “lower” to “higher” forms (like Aristotle’s
ladder) via inheritance of acquired characteristics. (Fig. 22.1c)

D. Darwin and Wallace and Evolution by Natural Selection

1. Species change over time, but they do not “progress.” They are related by a common ancestry.
(Fig. 22.1d)
2. A species does not have a single true “type.”
3. Individual variation is important; variation is what drives evolution.
4. This theory made predictions and was testable; that is, it was scientific.

22.2 The Pattern of Evolution: Have Species Changed, and Are They Related?
● Summarize evidence that supports the theory of evolution.
● Describe the evidence that supports change through time.
● Describe evidence that supports species descended from a common ancestor.
● Explain the concept of internal consistency in terms of evolution.

A. Two Predictions of Darwin’s Theory About Descent with Modification:

1. Species change through time.
2. Species are related by common ancestry.

B. Evidence of Change Through Time

1. The vastness of geologic time
a. A fossil is any trace of an organism that lived in the past. (Fig. 22.2)
b. The fossil record was initially organized based on the relative age of the fossils.
c. The geologic time scale
i. (1) Sedimentary rocks form layers over long times. These layers form in a
chronological sequence (the geologic time scale).
ii. (2) From the number of layers and the time it takes to deposit each one,
geologists realized that Earth must be very old.
 d. Radiometric dating enables us to date rocks directly.
i. (1) Earth is 4.6 billion years old.
ii. (2) The earliest signs of life are in rocks that are 3.4 to 3.8 billion years old.
2. 2. Extinction changes the species present over time.
a. The fossil record shows that more than 99 percent of all the species that have ever lived
are now extinct. (Fig. 22.3)
b. This is evidence that the species composition on Earth has changed over time.
3. 3. Transitional features link older and younger species.
a. Law of succession: Fossils found in a certain geographic region frequently resemble the
species currently living in that region. This is evidence that the extinct species are related
to existing species.
b. Fossils with transitional features (traits intermediate between those of older and
younger species) are compelling evidence that species change over time. Example: the
fins-to-feet transition (Fig. 22.4)
4. 4. Vestigial traits are evidence of change through time.
a. Vestigial traits are reduced incompletely developed structures that have no function, or
a reduced function, but are clearly related to functioning organs in related species. (Fig.
22.5)
b. The existence of these traits challenges the theory of special creation that organisms
were designed by a supernatural being and are static.
c. Biologists interpret the existence of these traits as evidence that organisms change over
time.
5. 5. Current example of change through time:
a. a. Biologists have documented hundreds of contemporary populations that are changing
in response to their environment.

C. Evidence of Descent from a Common Ancestor

1. 1. Similar species are found in the same geographic area.
a. Similar, but distinct, species are often found living close together in the same geographic
area, implying that they are linked by a common ancestor. Example: Galápagos
mockingbirds. (Fig. 22.6a)
b. These similar species can be diagrammed on a phylogenetic tree (a branching diagram
that indicates genealogy). (Fig. 22.6b)
2. 2. Similar species share homologies
a. a. Homology can be recognized and studied at three levels (Table 22.1) (Making Models
22.1):
i. (1) Genetic homology—similarities in DNA sequences
ii. (2) Developmental homology—similarities in the morphology of embryos and
the fate of embryonic tissues
iii. (3) Structural homology—similarities in the structure of body parts (EX.
Pentadactly limb)
b. b. The three levels of homology interact: Genetic homologies cause developmental
homologies, which cause structural homologies.
c. c. Hypotheses about homology can be tested experimentally
d. d. Homology is used extensively in contemporary biology. Examples: use of model
organisms, comparative genomics
3. Current example of descent from a common ancestor
a. Biologists have documented dozens of examples of populations undergoing speciation.
 b. EX. Galapagos finches

22.3 The Pattern of Evolution: How Does Natural Selection Work?

● Explain how natural selection causes evolution.
● Describe artificial selection.
● Summarize the criteria that define s natural selection (Darwin's postulates).
● Compare terms used in evolution with their use in everyday English.

A. Darwin’s Inspiration
1. Darwin crossbred pigeons to observe the effects of artificial selection. (Fig. 22.8)
2. Thomas Robert Malthus’s study of human population growth inspired the idea that there is a
“struggle for existence.”

B. Darwin’s Four Postulates

1. Individuals vary.
2. Some trait differences are heritable.
3. More offspring are produced than can survive.
4. Individuals with traits that confer an advantage are more likely to survive and reproduce.
5. Summary: Evolution by natural selection occurs whenever heritable variation leads to differential
success in survival and reproduction.

C. Evolutionary Definitions of Fitness, Adaptation, and Selection

1. Fitness is the ability of an individual to survive and reproduce, relative to other individuals in that
population.
2. Adaptation is a heritable trait that increases the fitness of an individual in a particular
environment, relative to other individuals lacking the trait.
3. Artificial selection is the process of breeders choosing characteristics in the animals or plants
they breed. Natural selection is a passive process by which differential reproduction is a result of
heritable variation.

Postulates of Evolution
1. Variation: members of a population often vary greatly in their traits
2. Inheritance: most traits are inherited from parents to offspring
3. Overproduction of offspring: specifies can produce more offspring than the environment can
support (i.e. who gets to live and who dies?)
4. Differential fitness: offspring with traits better matched to the environment will survive and
reproductive more effectively
* Evolution by natural selection occurs when heritable variation leads to differential success in survival
and reproduction

23.1 Null Hypothesis: The Hardy-Weinberg Principle

After reading Section 23.1, you should be able to:

● Genotype VS. Phenotype VS. Homozygous VS. Heterozygous
○ 2 alleles and 3 possible genotypes
● Apply the Hardy–Weinberg principle to determine if a population is evolving.
○ When unstable, the population is evolving
 ● Describe the gene pool concept.
● Explain what it means for a population to be in Hardy–Weinberg equilibrium.
● Summarize the assumptions made by the Hardy–Weinberg principle.

Reading Outline:
A. The gene pool concept and allele frequencies (Fig. 23.1)
1. The gene pool is all the gametes produced in one generation.
2. The symbols p and q are traditionally used to depict allele frequencies.
3. The frequencies must add up to 1. If there are just two alleles, p + q = 1.
4. Gametes are assumed to combine randomly.
a. Genotype frequencies in the offspring can be calculated based on probabilities of
gametes combining. (Fig. 23.2)
5. Deriving the Hardy–Weinberg principle (Quantitative Methods 23.1) (Fig. 23.3)
● A population's allele and genotype frequencies are inherently stable unless
evolutionary forces are acting upon the population
a. Consider a population in which all gametes combine randomly.
b. Prediction 1: Genotype frequencies in the offspring can be calculated from the
parental allele frequencies as follows:
(1) The predicted frequency of the offspring A1A1 genotype is p2.
(2) The predicted frequency of the offspring A1A2 genotype is 2pq.
(3) The predicted frequency of the offspring A2A2 genotype is q2.
(4) The frequencies of all genotypes add up to 1, so p2 + 2pq + q2 = 1.
c. Prediction 2: Offspring allele frequencies are the same as parental allele frequencies.
(1) In the absence of evolutionary forces, allele frequencies stay wherever they
were originally.
(2) Allele frequencies do not tend to move toward 0.5.
(3) Dominant alleles do not tend to increase in frequency.
6. For evolution to occur (that is, for allele frequencies to change), some outside factor must be
interfering with the random combination of gametes that the model assumed at the beginning.
7. Any population that does not match the two predictions is evolving, is experiencing
nonrandom mating, or both.

B. The Hardy–Weinberg model makes important assumptions.

1. For a population to be in Hardy–Weinberg equilibrium, there must be:
a. Random mating (with respect to the gene in question)
b. No natural selection
c. No genetic drift (no random allele frequency changes)
d. No gene flow via immigration or emigration
e. No mutation

C. How do biologists apply the Hardy–Weinberg principle to real populations?

1. The Hardy–Weinberg principle tells us what to expect if no evolution is occurring and if there
is random mating.
2. Case study 1: Are MN blood-type alleles in humans in Hardy–Weinberg equilibrium?
a. For every human population surveyed, genotypes at the MN locus satisfy the
Hardy–Weinberg equation. (Table 23.1)
 b. Therefore, the M and N alleles are not currently affected by any of the four
evolutionary mechanisms, and mating is random (i.e., humans do not choose their
mates based on blood type). Types of Selection
● Directional selection: favors traits that are at one extreme (EX. giraffe’s neck)
○ As this type of selection occurs more frequently, favorable traits become more and more
extreme resulting in distinct changes in allele frequency.
● Disruptive selection: selects against the average individual in a population (selects both
extremes) (ex. black and white oyster color, african swallowtail butterflies)
○ Does not affect mean
● Stabilizing selection: favors the intermediate variants (ex. infant mortality rate)
○ Does not affect mean
● Adaptation: structural, behavioral, or physiological adaptation (related to the biochemical
processes in an organism’s body)
● Differential reproduction: individuals within a population that are most adapted to the
environment are also the most likely to reproduce successfully
○ Reproductive process tends to strengthen the frequency of expression of heritable traits
across the population
○ Increase the number of alleles for desirable traits in the gene pool -> if environmental
conditions stay the same, the heritable traits are more commonly expressed
● Mutation: change in the DNA sequence of a gene resulting in a change of the trait (random
occurrence)
○ Change in population occurs very slowly over multiple generations and introduce new
genetic possibilities
● Genetic drift: change in the frequency of an existing gene variant in a population due to random
chance -> reduction in genetic variability (EX. Disease)
○ Occurs within finite separation populations, allowing each to develop their own distinct
gene pool
○ Founder effect: the loss of genetic variation that occurs when a new population is
established by a very small number of individuals from a larger population (EX. Amish)
■ Bottleneck: events that cause a population size to start to decline rapidly, leaving
a shallow pool of genetic traits from the surviving individuals (extreme type of
genetic drift)
● Due to extreme events or being the result of over-predation.
● Gene migration (flow): immgriation from one population migrated to a new population, causing
change in gene pool
○ Occasionally successful between members of a different but related species (hybrids) ->
increased variability
○ EX. a bee carrying pollen from one flower population to another, or a caribou from one
herd mating with members of another herd.
● Gene flow: genetic exchange with another population (reduction in genetic difference between 2
populations)

23.3 Natural Selection

After reading Section 23.3, you should be able to:

● Explain why natural selection violates the Hardy–Weinberg assumptions.
● Compare directional, stabilizing, disruptive, and balancing selection.
● Compare intersexual and intrasexual selection.
 ● Compare the models of selection in terms of their effect on phenotype and genetic variation.
● Define the fundamental asymmetry of sex.
● Describe intersexual selection.
● Describe the relationship between sexual dimorphism and sexual selection.

Reading Outline:

A. How does selection affect genetic variation?

1. Natural selection occurs in a wide variety of modes. (Table 23.2)
2. Mode 1: Directional selection
a. One extreme is favored, and the average phenotype (and the other extreme) is
selected against. (Fig. 23.6)
b. Directional selection changes the average value of a trait.
c. It reduces genetic variation. If continued for a long time, the favored allele becomes
“fixed” at 1.0, and the other allele(s) dies out.
d. It is often counterbalanced by selection on a different trait (countervailing selection
and fitness trade-offs).
e. Predict how genotype frequencies differ from Hardy-Weinberg equilibrium under
directional selection.
3. Mode 2: Stabilizing selection
a. The average phenotype is favored, and both extremes are selected against. (Fig. 23.7)
b. The average value of the trait does not change over time.
c. Stabilizing selection reduces genetic variation.
4. Mode 3: Disruptive selection
a. Both extremes are favored, and the average phenotype is selected against. (Fig. 23.8a)
Example: gill raker number in whitefish (Fig. 23.8b)
b. Disruptive selection is relatively rare.
c. It maintains genetic variation.
d. It plays a role in speciation—the generation of new species.
5. Mode 4: Balancing selection
a. No single allele has an advantage; instead, there is a balance among several alleles,
with each having advantages in certain situations. Examples: heterozygote advantage,
selection in variable environments, and frequency-dependent selection
B. Sexual selection
1. Sexual selection favors individuals with heritable traits that enhance their ability to attract
mates.
2. This includes selection both within the sex (intraspecific selection) and between the sexes
(intraspecific selection).
3. Theory: The fundamental asymmetry of sex (Bateman–Trivers theory)
a. Pattern: Sexual selection usually acts on males more strongly than females.
b. Process: In most species, females invest more in their offspring than males.
c. Predictions of the Bateman–Trivers theory
(1) Females should be choosy about mates.
(2) Males should compete with one another for mates.
(3) Sexual selection should act more strongly on males than on females.
4. Female choice for “good alleles”
a. Female birds often prefer colorful males, which is an indication of the male’s health
and diet (and presumably the quality of his genes).
 b. Sometimes females choose males for their ability to help care for the young.
5. Male–male competition
6. Sexual dimorphism results from sexual selection. (Fig. 23.12)
a. Because sexual selection tends to be much more intense in males than in females,
males tend to have many more traits that function only in courtship or in male–male
competition.
b. Sexual selection often results in sexual dimorphism. Sexual dimorphism is any trait
that differs between males and females.
c. Like inbreeding, sexual selection violates the assumptions of the Hardy–Weinberg
principle.
d. Unlike inbreeding, sexual selection causes evolution.

23.4 Genetic drift

After reading Section 23.4, you should be able to:

● Compare genetic drift to the other processes of evolution.
● Explain the effect of genetic drift on genetic variation.
● Explain the effect of genetic drift on fitness.
● Explain how sampling error causes genetic drift.
● Explain the founder effect.
● Explain the bottleneck effect.

A. Genetic drift is any change in the allele frequencies in a population that is due to chance (luck,
sampling error).
1. Genetic drift causes allele frequencies to drift up and down randomly over time.
B. Simulation studies of genetic drift
1. Genetic drift can be simulated by flipping a coin. (data in column 1, p. 483)
2. Computer simulations can model genetic drift over many generations. (Fig. 23.13)
a. Students should be able to examine the MN blood group genotype frequencies in
Table 23.1 and describe how drift could explain differences in genotype frequencies
among populations.
3. Key points about genetic drift:
a. Genetic drift is random with respect to fitness.
b. Genetic drift is most pronounced in small populations.
c. Over time, genetic drift can lead to the random loss or fixation of alleles.
C. Experimental studies of genetic drift
1. Bristle type in fruit flies
a. 96 small populations (8 individuals each), starting with equal frequencies of forked
bristles and normal bristles, were followed for 16 generations.
b. Four males and females from the F1 generation were randomly selected from each of
the 96 populations.
c. By the 16th generation, 73 percent of the populations had completely lost either the
forked-bristle or the normal-bristle allele.
D. What causes genetic drift in natural populations?
1. Founder effects on the green iguanas of Anguilla (Fig. 23.14a)
 a. Drift occurs when a group of individuals immigrate to a new geographic area and
establish a new population (founder event).
b. If the new population is small, the allele frequencies will likely be different from those
in the orig-inal population (founder effect).
2. Population bottleneck on Pingelap Atoll (Fig. 23.15a)
a. A bottleneck occurs when a disease outbreak, a natural catastrophe, or another event
causes a sudden reduction in population size.
b. The remaining individuals likely have different allelic frequencies than the original
population.
c. Example: the island of the color-blind (Pingelap Atoll)
(1) Only 20 people survived a typhoon and famine in 1775.
(2) The survivors happened to have a high frequency of an allele for total
color-blindness (allele CNGB 3).
(3) Today, many people on the island are completely color-blind. (Fig. 23.15b)

23.5 Gene Flow

After reading Section 23.5, you should be able to:

● Explain gene flow.
● Explain the effect of gene flow on genetic variation.
● Explain the effect of gene flow on fitness.
● Compare gene flow to the other processes of evolution.

A. Gene flow is the movement of alleles from one population to another. (Fig. 23.16)
B. Measuring gene flow between populations
1. Example: steelhead trout in Oregon (Fig. 23.17a)
a. Captive bred trout reduce the fitness of wild populations due to reduced gene flow.
(Fig. 23.17b)
C. Gene flow is random with respect to fitness.
1. Gene flow tends to equalize allele frequencies among populations.
a. For example, human migration across continents is homogenizing allelic frequencies in
human populations.

23.6 Mutation

After reading Section 23.6, you should be able to:

● Compare mutation to the other processes of evolution.
● Describe how mutations occur.
● Describe the effect of mutation on genetic variation.
● Explain the effect of mutation on fitness.
● Explain the importance of mutation to evolution.

A. Three ways mutations can occur to increase genetic diversity in populations.

1. Point mutations—a change in the nucleotide sequence in a stretch of DNA.
2. Chromosome-level mutations—this often results in gene duplication.
3. Lateral (Horizontal) gene transfer—transfer of genes from one species to another.
B. Mutation as an evolutionary process
1. Mutation happens too infrequently to cause dramatic changes in allele frequencies on its own.
a. Example: human mutation rates. It would take 4,000 years for a mutation to produce a
change in allele frequency of 1 percent.
2. However, when considered across entire genomes and combined with natural selection,
mutation becomes an evolutionary force.
C. Experimental studies of mutation
1. Study of mutation in Escherichia coli over 10,000 generations. (Fig. 23.18)
a. Relative fitness increased dramatically over time but in a stepwise pattern.
b. Each jump in fitness was caused by a novel mutation.
2. Students should be able to explain why deleterious mutations do not cause downward drops
in fitness in Figure 23.17.
D. Studies of mutation in natural populations
1. Lateral gene transfer—Pea aphids acquired the ability to generate carotenoids from the
genome of a fungal symbiont. (Fig. 23.19a)
2. Gene duplication—Once genes were transferred, genes were duplicated (and diversified) to
form the genome of the red pea aphid and subsequently deleted to be adaptive for the green
pea aphid. (Fig. 23.19b)

Quiz 2 Running Vocab List

● Phylogeny
● Systematics: discipline of biology that characterizes and classifies the relationships among all
organisms on Earth
○ Within systematics, taxonomy: practice of describing, naming, and classifying individual
species.
● Branch: A line representing a species or other taxon through time
● Root: The most ancestral branch in the tree
● Node (fork): A point within the tree where a branch splits into two or more branches; the node
represents the most recent common ancestor of the descendant groups
● Internal branch
● Polytomy: A node that depicts an ancestral branch dividing into three or more (rather than two)
descendant branches; usually indicates that insufficient data were available to resolve which taxa
are more closely related
● Outgroup: A taxon that diverged before the taxa that are the focus of the study; helps to root the
tree
● Terminal branch
● Tip: Endpoint of a branch; represents a living or extinct species or other taxon
● Synapomorphies: traits found in two or more taxa that is present in their most recent common
ancestor but missing in more distant ancestors
○ Monophyletic group: any group that forms an evolutionary unit including an ancestral
population and all of its descendants but no others (i.ee. Lineage or clade)
○ Non-monophyletic
■ paraphyletic: includes the ancestral population and some of its descents but not
all
■ polyphyletic: includes the ancestral population and some of its descents but not
all
 ● Convergent evolution: independent evolution of similar traits in distantly related organisms due
to adaptations to similar environmental pressures (ex. streamlined body and flippers in dolphins
vs ichthyosaur; wings in birds and insects; streamline appendages in shark, penguin, and
dolphins)
○ Homoplasy: traits are similar but not inherited from a common ancestor
○ Analogous structures: product of convergent evolution
● Divergent evolution: process by which two species evolve in diverse directions from a common
point due to differential selection pressure (EX. forelimbs in salamander and opossum; flowers in
angiosperms; pentadactyl limbs in human, cat, whale, and bat)
○ Homology: similarity of structure physiology or development of different species of
organisms based upon their descent from a common evolutionary ancestor
○ Homologous structures: structures that exist in two different species because they share
a common ancestry
● allopatric speciation: “different homeland” occurs when you have a physical barrier, but note
that it does not always lead to reproductive isolation
● sympatric speciation: “same homeland” (ex. Hawthorne fly)
● Autopolyploidy: 2+ chromosomes; same species (EX. self-fertilization, fusion of unreduced
gametes)
○ “Auto” = same
○ “Poly” = many
○ “Ploidy” = chromosome sets
● Allopolyploidy: 2+ chromosomes; different species (have different # of chromosomes)
○ Could not mate with the parents, but enough allopolyploid offspring are created, they
can mate with each other and produce a new species
● Can have hybridization without polyploidy, due to isolation
○ Prezygotic barriers: Temporal, Habitat, Mechanical, Gametic (differences in proteins on
gametes that prevent them from being able to recognize each other)
○ Postzygotic barriers:
■ Reduced hybrid viability: zygote will develop, but may not finish and will not
make it to life cycle stage where it will reproduce
■ Reduced hybrid fertility (EX. Horse + Donkey = Mule): offspring will survive, but
are sterile
■ Hybrid Breakdown (EX. Grass): adult is fertile at a low level and not able
reproduce effectively
● Adaptive radiation (EX. galapagos finches): new environment or change in environment that
opens up new resources

25.1 Tools for Studying Life's History: Phylogenetic Trees

● Use phylogenetic trees to answer biological questions.
● Interpret evolutionary relationships from phylogenetic trees.
● Draw phylogenetic trees from small data sets.
● Differentiate homology and homoplasy.
A. Tree basics

1. A phylogeny is an evolutionary history of a group of organisms.

2. A phylogenetic tree is a graphical summary of this history.
3. The tree of life is the most universal of all phylogenetic trees depicting the evolutionary
relationships among all living organisms.
4. Reading phylogenetic trees (Table 25.1)
a. Branches represent populations through time.
b. The tips of the branches represent specific taxa.
c. Nodes (forks) occur when an ancestral group split into multiple descendent groups.
d. The root is the most ancestral branch in the tree.
e. Outgroups help to root the tree by including a taxa that diverged prior to the focal
group.
f. A node that depicts an ancestral branch dividing into three or more descendant
branches is called a polytomy.
g. Branches of the tree can rotate at each node. (Making Models 25.1)
h. The number of nodes is not useful in determining relationships. (Making
Models 25.2)
B. How do biologists estimate phylogenies?

1. Creating the data matrix

a. Closely related species should share many characters, while more distantly related
species should share fewer characters. (Fig. 25.1a)
2. Using the data matrix to estimate a tree
a. The cladistic approach is based on synapomorphies (shared derived traits) that
identify monophyletic groups. (Fig. 25.1b)(Table 25.2)
b. Ancestral and derived traits are relative.
 c. Ultimately, trees with the best fit are those that exhibit the least amount of changes
(parsimony).
d. Cladistic analysis does not consider the length of branches, but other analyses
estimate this via genetic distance or time. (Table 25.3)
3. Using the alternative hypothesis that limbs arose separately in lizards and in the ancestors of
dogs and humans, students should be able to draw a revised tree (Fig. 25.1b) that shows five
character changes.
C. How can biologists distinguish homology from homoplasy?
1. Homology is similarity in a trait due to common ancestry.
2. Homoplasy is similarity in a trait for some reason other than common ancestry, such as
convergent evolution.
3. Are the flowers of water lilies and wild roses homologous or convergent?
a. Phylogenetic evidence—water lilies and wild roses have flowers because they
inherited these structures from a common ancestor that also had flowers.
b. Structural evidence—although flower structure is diverse, most flowers are built upon
the same general template.
c. Genetic and developmental evidence—the genetic toolkit and developmental pattern
of floral structures are similar.
d. The data provide strong evidence that flowers in diverse types of plants are
homologous.
4. Are streamlined bodies in dolphins and ichthyosaurs homologous or convergent?
a. The streamlined bodies are convergent evolution as natural selection favored similar
solutions to the problems posed by a similar way of making a living. (Fig. 25.3)

24.1 How are Species Defined and Identified?

● Compare mechanisms of reproductive isolation.
● Describe methods of prezygotic reproductive isolation.
● Describe methods of postzygotic reproductive isolation.
● Compare the advantages and disadvantages of different species concepts.
● Explain the biological species concept.
● Explain the morphospecies concept.
● Explain the phylogenetic species concept.
Please also read the Introduction section that is at the beginning of the Chapter (includes Figs 24.1 and
24.2)

A. Speciation occurs when a single ancestral group splits into two or more species.
1. Speciation results from genetic isolation and genetic divergence.
a. If gene flow ends (genetic isolation), allele frequencies in isolated populations are free
to diverge via mutation, genetic drift, and selection.
b. If the populations diverge enough, they become new species.
B. A species is an evolutionarily independent population or group of populations.
1. Biologists use different sets of criteria to identify species.
C. The biological species concept
1. Species are defined by reproductive isolation.
2. Populations are reproductively isolated if they fail to interbreed or to produce viable, fertile
offspring. (Table 24.1)
a. Prezygotic isolation mechanisms prevent fertilization.
 b. Postzygotic isolation mechanisms prevent survival or reproduction of the hybrid
offspring.
3. Reproductive isolation cannot be evaluated in fossils, asexual species, or species whose
ranges do not overlap.
D. The morphospecies concept
1. Species are defined by differences in size, shape, or other morphological features
(polymorphic).
2. The morphospecies concept is widely applicable and can be used for fossil species and
asexual species.
3. The morphospecies concept cannot identify cryptic species, and it is subjective.
E. The phylogenetic species concept
1. A species is defined as the smallest monophyletic group on the tree of life.
a. A monophyletic group consists of an ancestral population, all of its descendants, and
only its descendants. (Fig 24.3)
b. A monophyletic group is identified by synapomorphies (homologous traits unique to
that lineage)
c. Example: elephants (Fig. 24.4)
2. Advantages of the phylogenetic species concept:
a. It can be applied to any population.
b. It is logical because populations are monophyletic only if they are independent of one
another and isolated from gene flow.
3. The phylogenetic species concept typically recognizes many more species than any other
species concept.
4. In actual practice, researchers use all three species concepts: biological, morphospecies, and
phylogenetic. (Table 24.2)

24.2 Isolation and Divergence in Allopatry

● Use examples to explain the process of allopatric speciation.
● Define allopatric speciation.
● Explain how processes of evolution affect speciation.
● Explain allopatric speciation by dispersal.
● Explain allopatric speciation by vicariance. In class notes
● “Inflation causes devaluation” -> look at subspecies instead of overall species

A. Speciation that begins with physical isolation is called allopatric speciation.

1. Physical isolation occurs in two ways.
a. Dispersal—a population can colonize a new habitat. (Fig. 24.5a)
b. Vicariance—a new physical barrier can split a widespread population into two or
more isolated groups. (Fig. 24.5b)
B. Allopatric speciation by dispersal
1. Example: Galápagos finches
a. A population of ground finches colonized a new island. Later they were found to have
larger beaks than the original population.
2. Colonization, followed by drift and selection, is thought to be responsible for speciation in
many groups.
 3. Concept check! Can you apply the model in Figure 24.4a to this example? What does the
small population on the right side of the model represent? What does the red color represent?
How can you modify the model to show that gene flow is still occurring?
C. Allopatric speciation by vicariance
1. Example: trumpeters
a. Many species of trumpeters within the Amazon basin are closely related. (Fig. 24.6)
b. This pattern indicates that the formation of the Amazon basin via the rising Andes
Mountains was a vicariance event that separated the original trumpeter species, which
then caused speciation.

24.3 Isolation and Divergence in Sympatry

● Use examples to explain the process of sympatric speciation.
● Define sympatric speciation.
● Explain sympatric speciation by disruptive selection.
● Explain sympatric speciation by polyploidization.

A. Sympatric populations live in the same area.

1. Traditionally, biologists thought that speciation could not occur among sympatric populations
because gene flow is possible. (Fig. 24.7)
B. Sympatric speciation by disruptive selection
1. Populations that are not geographically isolated may become reproductively isolated by
adapting to different ecological niches via disruptive selection.
2. Disruptive selection for ecological niche in flies
a. Example: killer whales (Table 24.3)
b. Killer whales in the Pacific Northwest vary in terms of the group size in which they
live, whether they are transient or resident, and what they look like.
c. Transients occur in smaller groups and have pointier dorsal fins.
d. Different feeding cultures indicate different ecological niches.
e. Transients and residents also differ in how they communicate.
f. Concept check! Can you hypothesize why natural selection would favor divergence
based on the described observations of different groups of killer whales?
C. Sympatric speciation by polyploidization
1. In plants, a mutation known as polyploidy reduces gene flow between normal and
mutant plants.
a. Polyploidy is a condition of having more than two complete sets of chromosomes.
b. Tetraploid (4n) individuals cannot mate with diploid (2n, normal) individuals
because the resulting triploid offspring are sterile.
c. Because polyploidy reduces gene flow, it can and does lead to speciation.
2. Autopolyploidy (Fig 24.8a)
a. Autopolyploidy is a doubling of the chromosome number in the offspring of one
species.
b. This can result in a new tetraploid species. Example: maidenhair ferns
c. Concept check! Can you explain the origin of a tetraploid grape with extra-large fruit
from a diploid population with smaller fruit?
3. Allopolyploidy (Fig. 24.8b)
 a. Allopolyploidy occurs when two diploid species hybridize and the hybrid offspring
experiences a mutation that doubles the chromosome number so that it can produce
gametes.
b. Like autopolyploidy, this can result in a new, tetraploid species. Example: Tragopogon
(Fig. 24.9)
c. Concept check! Students should be able to explain how a cross between Emmer
wheat, a tetraploid, and a wild, diploid wheat gave rise to the hexaploid bread wheat
grown throughout the world today.
4. Why is speciation by polyploidy so common in plants?
a. In plants, gametes are produced from tissues that have undergone many rounds of
mitosis, making mutations (like chromosome doubling) more likely. This increases the
variation in the population.
b. Many plants can self-fertilize, making it possible for a rare individual with diploid
gametes to produce tetraploid offspring.
c. Hybridization between plant species is common. Polyploids have a higher level of
heterozygosity than diploids.

QUIZ 3 VOCABULARY
●

26.1 Why Do Biologists Study Bacteria and Archaea?

● Explain why bacteria and archaea are considered the most important, diverse, and abundant
organisms on Earth.
● Describe the characteristics of prokaryotes.
● Explain how prokaryotes live in extreme environments.
● Describe the medical importance of disease-causing bacteria.
● Explain the role of bacteria in bioremediation.

A. Bacteria, Archaea, and Eukarya are the three largest branches on the tree of life.
1. Bacteria and archaea may look similar at first glance, but they are very different.
2. Similarities: All bacteria and archaea are prokaryotic and unicellular (lack membrane bound
nucleus), and they help form the microbiome (a community of microbes that naturally inhabits a
particular area and encompasses all the genetic material contained within it)
3. Fundamental differences: (Table 26.1)
a. Bacteria have cell walls made of peptidoglycan.
b. Archaea have unique phospholipids (the hydrocarbon tails of the
phospholipids are made from isoprene) in the cell membranes.
c. Bacteria and archaea have different ribosome and RNA polymerase structures.
d. Archaea are more closely related to Eukarya than to Bacteria.

A. Biological impact
1. Bacteria and archaea are amazingly abundant.
a. A mere teaspoon of soil contains billions of microbial cells.
b. A liter of seawater contains a population of microbes equivalent to that of a large
human city.
c. Microbes living under the ocean may make up to 10 percent of the world’s total
 living biomass.
2. They are found in every possible environment.
3. They are very diverse, and we are still discovering entire new phyla.
B. Some microbes thrive in extreme environments.
1. Extremophiles are bacteria that live in unusual environments.
a. For example, there are bacteria that live at a pH less than 1.0, at temperatures of 0°C
under the ice, and in water 5–10 times saltier than seawater. (Fig. 26.1)
2. Studying extremophiles may help us understand the origin of life, since life probably evolved
in a high-temperature, anoxic environment.
3. Astrobiologists use extremophiles as model organisms in the search for extraterrestrial life.
4. Extremophiles are useful in certain commercial and research applications.
a. For example, the heat-tolerant enzyme that is necessary for PCR (the DNA-copying
technique fundamental to most genetic research) is from an extremophile found in hot
springs in Yellowstone National Park.
C. Medical importance
1. Some bacteria are pathogenic, meaning that they cause disease. (Table 26.2)
a. Pathogenic forms come from several different lineages in the domain Bacteria.
b. Pathogens tend to affect tissues at entry points into the body.
2. Koch’s postulates: Koch proposed four criteria that had to be met to prove that a specific
microbe causes a certain disease (they are still used today):
a. The microbe must be present in individuals suffering from the disease and absent in
healthy individuals
b. The microbe must be isolated and grown in pure culture.
c. Injection of the microbe (from the pure culture) into a healthy animal should cause
the disease symptoms to appear.
d. The microbe should be isolated again from the diseased animal and shown to be
identical in size, shape, and color to the original microbe.
3. The germ theory of disease
a. The germ theory is based on Koch’s postulates.
b. The germ theory states that infectious diseases are caused by microbes (microscopic
organisms).
c. Infectious diseases are spread in three main ways:
(1) From person to person
(2) From bites of insects or animals
(3) From ingesting contaminated food or water, or environmental exposure
d. The germ theory’s immediate impact was in improving sanitation, greatly reducing
mortality due to infectious disease.
4. What makes some bacterial cells pathogenic?
a. Virulence, or the ability to cause disease, is a heritable trait that varies among
individuals in a population.
b. Current research is identifying the genes responsible for virulence in a wide variety of
bacteria.
5. Some pathogenic bacteria produce resistant endospores
a. Endospores are tough, thick-walled, dormant structures formed during times of
environmental stress.
b. Endospores contain a copy of the cell’s DNA, RNA, ribosomes, and essential enzymes.
(Fig. 26.2)
c. When conditions become favorable, endospores resume growth as normal cells.
 6. Antibiotics are molecules that kill bacteria.
a. Since their development in the late 1920s, antibiotics have been very useful in
combating infectious disease.
b. Unfortunately, many pathogens are evolving resistance to antibiotics.
c. Biofilms can provide protective structures that shield bacteria from antibiotics.
D. Role in bioremediation
1. Some of the most serious pollutants are hydrophobic compounds that accumulate in sediment
and in the bodies of living organisms.
2. Bioremediation strategies use bacteria to break down these compounds.
a. Fertilization of contaminated sites encourages the growth of whatever existing
bacteria are already on site. These bacteria often degrade the toxic compounds.
b. “Seeding” adds specific bacteria that are known to use that pollutant as a food
source, producing a nontoxic by-product.

26.2 How Do Biologists Study Bacteria and Archaea?

● Describe the methods used to study bacteria and archaea.
● Describe how metagenomics is used to study prokaryotes.
● Explain the relationship between microbiomes and human health.
● Explain how phylogenies are used to study relationships among prokaryotes.
● Reading Outline:

A. Using enrichment cultures

1. Enrichment cultures provide a specific set of living conditions (food, temperature, etc.) and
can grow large populations of certain bacteria and archaea.
2. Most bacteria and archaea species were discovered when they were grown in a culture in a
lab.
3. Example: discovering bacteria from the depths of Earth (Fig. 26.3)
a. Samples were taken from 860 to 2,800 meters below Earth’s surface, where
temperatures reach 85°C.
b. Scientists hypothesized that if anything were living down there, it would produce
magnetite as a by-product of cellular respiration.
c. Magnetite did appear in cultures, and microscopy confirmed the presence of
previously unidentified thermophiles (bacteria that grow at only high temperatures).
B. Using metagenomics
1. Metagenomics allows biologists to name and characterize organisms that have never been
seen and investigate biological processes.
2. DNA is sequenced directly from a small sample from a habitat (soil, water, etc.). The DNA
sequences are then compared to known sequences to determine whether any previously
undiscovered species exist in the sample. (Fig. 26.4)
3. Metagenomics revealed in one study the similarity and differences in fecal bacteria across
125 subjects.
a. Most of the 1,000 species were found across all subjects, but some subjects
contained uncommon species.
b. The vast majority of bacterial species were from three phyla: Bacteroidetes,
Firmicutes, and Actinobacteria.
c. Many of the bacterial genes across the species were shared by all human subjects,
suggesting the critical importance that bacteria play in human physiology.
C. Evaluating molecular phylogenies
1. Ribosomal RNA sequences have shown that the tree of life has three major lineages: Bacteria,
Archaea, and Eukarya.
a. Archaea are more closely related to Eukarya than to Bacteria.
2. Further analysis has identified several monophyletic groups within each of these domains.
3. Bacteria and Archaea both form monophyletic groups including a number of phyla. (Fig. 26.5)

26.3 What Themes Occur in the Diversification of Bacteria and Archaea

● Describe reproductive, morphological, and metabolic diversity among prokaryotes.
● Explain how genetic variation is introduced in prokaryotes.
● Describe the structural features of prokaryotes.
● Explain the metabolic diversity among prokaryotes.
● Explain how ecological diversity impacts the environment.

A. Genetic variation through gene transfer

1. Gene transfer occurs in three ways:
a. Transformation—when bacteria or viruses naturally take up DNA from the
environment (Fig. 26.6a)
b. Transduction—when viruses pick up DNA from one prokaryotic cell and transfer it to
another cell (Fig. 26.6b) (bacteriophage ALWAYS means transduction)
c. Conjugation—when genetic information is transferred by direct cell-to-cell contact
2. Conjugation is often followed by plasmid transfer. A plasmid is copied in one cell and
transferred to another cell. (Fig. 26.7a)
3. Conjugation can also result in genetic recombination—the plasmid becomes integrated into
the main bacterial chromosome (Fig. 26.7b)
B. Morphological diversity
1. Size, shape, and motility (Fig. 26.8)
a. Bacteria vary greatly in size. For example, more than a billion of the smallest
bacterium could fit inside the largest bacterium.
b. Bacteria may be filaments, spheres, rods, chains, or spirals.
c. Many bacteria can swim or glide.
2. Cell wall composition (Fig. 26.9)
a. Gram-positive bacteria have a cell wall with abundant peptidoglycan, which stains
dark purple when exposed to a Gram stain. (Fig. 26.10a)
b. Gram-negative bacteria have a cell wall with a thin layer of peptidoglycan
surrounded by a phospholipid bilayer. They stain light pink. (Fig. 26.10b)
- Gram-negative bacteria are resistant to multiple drugs and are increasingly
resistant to most available antibiotics.
- Peptidoglycan prevents osmotic lysis in the hypotonic environment in which
most bacteria live.
c. Gram stain analysis can predict sensitivity to certain drugs.
(1) Gram-positive bacteria are often sensitive to penicillin-like drugs that
disrupt peptidoglycan synthesis.
(2) Gram-negative bacteria are more likely to be affected by drugs that target
bacterial ribosomes.
C. Metabolic diversity
1. Bacteria and archaea are astonishingly diverse in the ways they acquire energy to make ATP
and the carbon compounds they can use as building blocks.
2. There are three ways to acquire energy to produce ATP:
a. Phototrophs use light energy to energize electrons, producing ATP by
photophosphorylation (light reactions of photosynthesis).
b. Chemoorganotrophs oxidize organic molecules with high potential energy, such as
sugars (cellular respiration, fermentation).
c. Chemolithotrophs oxidize inorganic molecules with high potential energy, such as
ammonia or methane (usually via cellular respiration).
3. There are two ways to acquire carbon:
a. Autotrophs use carbon dioxide or methane to build their own carbon-containing
compounds.
b. Heterotrophs acquire carbon-containing compounds from other organisms.
4. Overall, there are six major “feeding strategies” (the six possible combinations of three
methods of acquiring energy and two methods of acquiring carbon) (Table 26.3)
a. Plants, animals, fungi, and other eukaryotes use only two strategies.
b. Bacteria and archaea use all six.
5. Producing ATP via cellular respiration: variation in electron donors and acceptors
a. In cellular respiration, electrons are moved from molecules with high potential energy
and gradually “stepped down” to a molecule with low potential energy, using the
released energy to make ATP. (Fig. 29.11)
b. Eukaryotes are chemoorganotrophs that use a sugar like glucose as the electron
donor and oxygen as the final electron acceptor.
c. Many bacteria and archaea are chemolithotrophs that use an electron donor that is
not a sugar and often an electron acceptor that is not oxygen. (Table 26.3)
(1) The electron donor may be hydrogen molecules, hydrogen sulfide, ammonia,
or methane.
(2) The electron acceptor may be sulfate, nitrate, carbon dioxide, or ferric ions.
6. Producing ATP via fermentation: variation in substrates
a. Fermentation is a strategy for making ATP from organic molecules that requires a
separate electron acceptor.
b. Fermentation is less efficient than respiration in making ATP.
c. Some bacteria ferment glucose to either ethanol or lactic acid.
d. Other bacteria use a variety of other organic compounds as fermentable substrates.
Examples: ethanol, fatty acids, complex carbohydrates, proteins, amino acids, lactose.
7. Producing ATP via photophosphorylation: variation in electron sources and pigments
a. There are three forms of photophosphorylation:
(1) Light activates a pigment that transports protons across a membrane, driving
the synthesis of ATP via chemiosmosis.
(2) Geothermal radiation can be used instead of light.
(3) Light can be absorbed by pigments that raise electrons to high-energy states.
The electrons are stepped down with electron transport chains, and the energy
released is used to make ATP.
b. The last mode of photophosphorylation uses electron transport chains that require a
source of electrons.
(1) Plants and cyanobacteria use oxygenic photosynthesis. This means they use
water as the source of electrons and produce oxygen as a by-product.
 (2) Many bacteria use anoxygenic photosynthesis, using a molecule other than
water as the source of electrons. Examples: hydrogen sulfide, ferrous iron. (They
also produce by-products other than oxygen.)
8. Obtaining building-block compounds: variation in pathways for fixing carbon
a. Autotrophs can build their own carbon compounds.
(1) Plants (and cyanobacteria) fix CO2 with the enzymes of the Calvin cycle.
(2) Some bacteria also fix CO2 but use different enzymatic pathways to do
so¾that is, not the Calvin cycle.
(3) Some bacteria use a molecule other than CO2 as the starting point.
Examples: methane, carbon monoxide, methanol
b. Heterotrophs obtain organic compounds from other organisms.
(1) Animals, fungi, and many bacteria and archaea use this strategy.
C. Ecological diversity and global impacts
1. Bacteria and archaea have altered the chemical composition of the oceans, the atmosphere,
and terrestrial environments for billions of years.
2. The oxygen revolution
a. No free O2 existed in Earth’s atmosphere for 2.3 billion years.
b. Cyanobacteria were the first organisms to perform oxygenic photosynthesis, and they
are responsible for the appearance of oxygen in Earth’s atmosphere. (Fig. 26.12)
(1) The fossil record shows that cyanobacteria first became numerous in oceans
2.7 to 2.5 billion years ago.
(2) Oxygen concentrations began to increase 2.3 to 2.1 billion years ago.
c. Once O2 was abundant, other organisms could use it as an electron acceptor. The
evolution of aerobic respiration was a crucial event in the history of life. (Fig. 26.13)
3. Nitrogen fixation and the nitrogen cycle
a. Plant growth is often limited by the availability of nitrogen, but plants cannot use
molecular nitrogen (N2) from the atmosphere.
(1) Some bacteria absorb N2 from the atmosphere and fix or reduce it to NH3,
ammonia, a form that plants can use.
(2) Other bacteria and archaea convert ammonia to nitrates and nitrites,
resulting in a complex nitrogen cycle. (Fig. 26.14)
b. Students should be able to provide a plausible explanation of what the composition
of the atmosphere and what the nitrogen cycle might be like if prokaryotes did not exist.
4. Nitrate pollution
a. Most farmers use synthetic fertilizers, which often contain ammonia, to add nitrogen
to soils and increase crop yields.
b. Bacteria convert the ammonia in fertilizer runoff into nitrates.
c. This has led to worldwide pollution of aquatic ecosystems with excessive nitrates,
which causes overgrowth of algae and results in anoxic “dead zones.” (Fig. 26.15)

27.3 What Themes Occur in the Diversification of Protists?

● Describe the life history innovations that evolved in protists.
● Explain how endosymbiosis lead to the origin of mitochondria and chloroplasts.
● Explain how the plasma membrane may have played a key role in the origin of nuclei.
● Describe the ways by which protists obtain nutrients.
● Explain how protists move.
● Explain the role of “alternation of generations” in the life cycle of protists.
27.3 What Themes Occur in the Diversification of Protists?
A. What morphological innovations evolved in protists?
1. All eukaryotes alive today have (1) either mitochondria or mitochondrial genes, (2) a nucleus
and endomembrane system, and (3) a cytoskeleton.
2. Early eukaryotes were probably single-celled organisms with mitochondria, a nucleus and
endomembrane system, and a cytoskeleton, but no cell wall.
3. Endosymbiosis and the origin of the mitochondrion
a. The endosymbiosis theory (Lynn Margulis, 1970s) proposes that mitochondria
evolved from an aerobic bacterium that was engulfed by an anaerobic eukaryotic cell.
(Fig. 27.8)
(1) This became a mutually beneficial symbiosis: The host supplied the
bacterium with protection and carbon compounds, and the bacterium produced
much more ATP than the host could produce on its own.
b. Many lines of evidence now support this theory.
(1) Mitochondria are similar in size to a-proteobacteria.
(2) They divide independently of the host cell, and they divide by fission, as
bacteria do.
(3) They have their own ribosomes and synthesize their own proteins, and the
ribosomes are similar in many ways to bacterial ribosomes
(4) They have double membranes, as would be expected if they were engulfed
by another cell.
(5) They have their own chromosomes, which are circular and similar to
bacterial chromosomes.
c. The most conclusive evidence is that mitochondrial genes are very closely
related to the genes from a-proteobacteria
4. Endosymbiosis and the origin of the chloroplasts
a. All photosynthetic protists have chloroplasts.
b. An extension of the endosymbiotic theory contends that the eukaryotic chloroplast
originated when a protist engulfed a cyanobacterium.
c. Many lines of evidence support this:
(1) Chloroplasts have the same list of bacteria-like characteristics presented
earlier for mitochondria.
(2) They contain circular DNA containing genes extremely similar to genes found
in various species of cyanobacteria
(3) The photosynthetic organelle of glaucophyte algae have an outer layer
containing the same peptidoglycan found in cyanobacteria.
(4) There are many examples of endosymbiotic cyanobacteria living inside cells
of protists or animals today.
d. To explain the fact that many protists have chloroplasts containing multiple layers of
membrane, researchers proposed the process of secondary endosymbiosis—an
organism engulfs a photosynthetic eukaryotic cell and retains the chloroplast.(Fig. 27.9)
e. Figure 27.10 shows where primary and secondary endosymbiosis occurred in the
phylogenetic tree of eukaryotes.
f. Explain how the primary and secondary endosymbiosis events introduced in this
chapter represent the most massive lateral gene transfers in the history of life, in terms
of number of genes moved at once. (Chapter 20, lateral gene transfer)
5. The nuclear envelope
 a. The nuclear envelope likely arose as infoldings of the plasma membrane that also
gave rise to
the endoplasmic reticulum. (Fig. 27.11)
b. Evidence: Infoldings of the plasma membrane occur in some extant bacteria, and the
nuclear envelope and ER of today’s eukaryotes are continuous.
c. Students should be able to explain why the above observations support the infolding
hypothesis.
d. The nuclear envelope allowed for the separation of transcription and translation.
e. This enabled alternative splicing and gave early eukaryotes more ways to control gene
expression.
6. Structures for support and protection (for your interest, not assessment)
a. The diversification of protists has been associated with the evolution of innovative
structures for support and protection. For example:
(1) Glasslike shells in a box-and-lid arrangement (diatoms) (Fig. 27.12a)
(2) A cell wall made of cellulose plates (dinoflagellates) (Fig. 27.12b)
(3) Chambers of calcium carbonate (foraminiferans) (Fig. 27.12c)
(4) Coverings of tiny pebbles (other foraminiferans and some amoebae)
(5) An internal support rod (parabasalids)
(6) A collection of protein strips under the plasma membrane (euglenids)
(7) Saclike structures (alveolates)
7. Multicellularity
a. Multicellular organisms contain more than one cell and have cells that are specialized
for different functions and express different genes.
b. The vast majority of multicellular species are eukaryotes.
c. Multicellularity evolved independently in several eukaryotic lineages: green plants,
fungi, animals, brown algae, slime molds, and red algae.
B. How do protists obtain food?
1. Protists have three ways of feeding: ingesting packets of food, absorption of molecules
directly from the environment, and photosynthesis.
a. Some species of protists use multiple feeding methods, and all three methods may
occur within a single lineage. Example: alveolates
2. Ingestive feeding
a. The large cell size of protists enabled some of them to develop a unique feeding
strategy: ingesting other organisms (ingestive feeding).
b. Ingestion can occur by eating live or dead organisms or scavenging loose bits of
organic debris.
c. Protists that feed by phagocytosis typically lack a cell wall and can move their plasma
membranes around their prey using pseudopodia. (Fig. 27.13a)
d. Some ingestive feeders sit and wait for prey to come by or have cilia that move the
environment by them. (Fig. 27.13b)
3. Absorptive feeding
a. Some absorptive-feeding protists are decomposers and feed on detritus (dead organic
matter).
b. Others live inside other organisms.
(1) Absorptive feeders that damage their hosts are called parasites.
4. Photosynthesis
a. Organisms that produce their own food through photosynthesis are called
autotrophs.
 b. Organisms that ingest or absorb food are called heterotrophs.
C. How do protists move?
1. Amoeboid motion is a sliding movement produced by extensions of the cell, called
pseudopodia, into which the cytoplasm streams. (Fig. 27.14)
2. Other protists move using cilia or flagella.
a. Flagella and cilia are identical in structure; each is composed of nine sets of doublet
microtubules and two central, single microtubules.
b. Flagella are long and usually single or paired (Fig. 27.15a). Cilia are short and
numerous. (Fig. 27.15b)
3. Even closely related protists can use very different forms of locomotion.
D. How do protists reproduce? (Note: We will likely save this for Wednesday, but I'm including it here to
keep it with Section 27.3)
1. Sexual reproduction evolved in protists and is one of the most significant evolutionary
innovations of the eukaryotes.
a. Asexual reproduction occurs via mitosis and cell division (protists) or fission (bacteria,
archaea). Offspring are genetically identical to the parents.
b. Sexual reproduction occurs via meiosis and fusion of gametes. Offspring are
genetically different from the parents.
2. Sexual versus asexual reproduction
a. Genetically variable offspring have a better chance of surviving in a changing
environment.
b. Pathogens and parasites are highly variable aspects of the environment because they
evolve quickly. Thus, sexual reproduction may primarily be an adaptation to fight disease
and parasites.
3. Students should be able to evaluate and explain whether it is consistent with the observation
that many protists undergo meiosis only when food is scarce or population density is high.
4. Lifecycles -- haploid versus diploid dominated
a. Virtually every aspect of a lifecycle is variable among protists.
b. The evolution of meiosis created a distinction between haploid and diploid phases in
life cycles.
c. In the diploid-dominant life cycle, meiosis occurs in the mitotically produced offspring
rather than the zygote, and gametes are the only haploid cells in the lifecycle. (Fig.
27.16a)
d. The diploid phase is longer and more prominent than the haploid phase. (Fig. 27.16a)
(Making Models 27.1)
5. Lifecycles -- alternation of generations (Fig. 27.17)
a. Alternation of generations is a type of lifecycle that includes both multicellular
haploid and multicellular diploid phases.
b. Diploid sporophytes produce haploid spores by meiosis; haploid gametophytes
produce haploid gametes by mitosis.

Q4 27.2 How Do Biologists Study Protists?

B. Evaluating molecular phylogenies

1. DNA sequence analysis has demonstrated that the seven major eukaryotic groups are indeed
monophyletic. (Fig. 27.7) (BioSkills 13)
 2. Current data suggest that the first major split in the eukaryotic tree was between the
Unikonta (one flagellum) and the Bikonta (two flagella).

Q4 27.3 What Themes Occur in the Diversification of Protists?

A. What morphological innovations evolved in protists?

7. Multicellularity
a. Multicellular organisms contain more than one cell and have cells that are specialized
for different functions and express different genes.
b. The vast majority of multicellular species are eukaryotes.
c. Multicellularity evolved independently in several eukaryotic lineages: green plants,
fungi, animals, brown algae, slime molds, and red algae.
D. How do protists reproduce?
1. Sexual reproduction evolved in protists and is one of the most significant evolutionary
innovations of the eukaryotes.
a. Asexual reproduction occurs via mitosis and cell division (protists) or fission (bacteria,
archaea). Offspring are genetically identical to the parents.
b. Sexual reproduction occurs via meiosis and fusion of gametes. Offspring are
genetically different from the parents.
2. Sexual versus asexual reproduction
a. Genetically variable offspring have a better chance of surviving in a changing
environment.
b. Pathogens and parasites are highly variable aspects of the environment because they
evolve quickly. Thus, sexual reproduction may primarily be an adaptation to fight disease
and parasites.
3. You should be able to evaluate and explain how this is consistent with the observation that
many protists undergo meiosis only when food is scarce or population density is high.
4. Lifecycles -- haploid versus diploid dominated
a. Virtually every aspect of a lifecycle is variable among protists.
b. The evolution of meiosis created a distinction between haploid and diploid phases in
lifecycles.
c. In the diploid-dominated lifecycle, meiosis occurs in the mitotically produced
offspring rather than the zygote, and gametes are the only haploid cells in the lifecycle.
(Fig. 27.16a)
d. The diploid phase is longer and more prominent than the haploid phase. (Fig. 27.16a)
(Making Models 27.1)
5. Lifecycles -- alternation of generations (Fig. 27.17)
a. Alternation of generations is a type of lifecycle that includes both multicellular
haploid and multicellular diploid phases.
b. Diploid sporophytes produce haploid spores by meiosis; haploid gametophytes
produce haploid gametes by mitosis.

28.1 Why Do Biologists Study Green Algae and Land Plants?

● Summarize the ecosystem services and foods, medicines, and materials plants provide humans.
● Explain the roles of plants in maintaining healthy ecosystems.
● Describe the roles of plants in the production of food, fuel, materials, and medicine.

A. Plants provide ecosystem services.

 1. Plants improve the atmosphere, surface water, and soil in ways that benefit other organisms.
2. Plants produce oxygen.
3. Plants build and hold soil, and devegetation reverses that process. (Fig. 28.1)
4. Plants hold water and moderate climate.
5. Plants are primary producers.
a. Plants are the primary food producers on Earth.
b. Plants produce sugars and oils, via photosynthesis, that provide the foundation for
virtually all food chains.
c. Herbivores eat plants, carnivores eat herbivores, and omnivores eat many sources of
food.
d. Plants are the key to the carbon cycle on land.
(1) Plants take CO2 from the atmosphere and use it to make sugar.
(2) Plants fix more CO2 than they generate.
6. Students should be able to explain the potential impacts of deforestation.
B. Plants provide humans with food, fuel, fiber, building materials, and medicines.
1. Food
a. Crop plants were domesticated at several different locations between 10,000 and
2,000 years ago. (Fig. 28.2a)
b. Humans gradually changed the characteristics of food plants via artificial selection.
Example: kernel size in maize (Fig. 28.2b)
2. Fuel
a. For thousands of years, wood was the primary source of fuel used by humans.
b. In recent centuries, coal—formed by plants that lived hundreds of millions of years
ago—has replaced wood as our primary energy source.
3. Fiber and building materials
a. Cotton and other plant fibers are used in clothing and other cloth-based household
items.
b. Woody plants are used to make lumber and paper.
4. Medicines
a. Plants contain many compounds helpful in fighting disease. (Table 28.1)

28.2 How Do Biologists Study Green Algae and Land Plants?

● Analyze research strategies for studying key features of green plants and the relationships
among the major groups.
● Analyze key morphological traits of plants.
● Describe the use of the fossil record in studying land plants.
● Evaluate the molecular phylogeny of the Plantae.
A. Analyzing morphological traits
1. Similarities between green algae and land plants
a. Both have chloroplasts with chlorophyll a and b (photosynthesis) and beta-carotene.
b. They have similar structure and composition of their thylakoids, cell walls, sperm,
and peroxisomes.
c. They both synthesize starch as a storage product.
d. The ancestor of land plants was probably a multicellular green alga that lived in
freshwater, similar to stoneworts. (Fig. 28.3)
2. Major morphological differences among land plants (transitioned to terrestrial env)
 a. Nonvascular plants lack vascular tissue (rely on diffusion) (Fig. 28.4a)
● Rate of diffusion limit size and rely on spores
b. Seedless vascular plants have vascular tissue but do not make seeds. (Fig. 28.4b)
c. Seed plants (evolved once) have vascular tissue and make seeds. (Fig. 28.4c, d) ->
Gymnosperm vs. Angiosperms
B. Using the fossil record (Fig. 28.5)
1. The first-known green algae lived between 700 and 725 million years ago (mya) in freshwater
habitat, when oxygen levels began to rise.
2. Origin of land plants
a. The first-known land plants occurred 475 mya.
b. These fossils resemble today’s land plants because they have sheets of waxy
cuticle, spores with sporopollenin-containing walls, and spores contained within
specialized structures called sporangia.
3. Silurian–Devonian explosion
a. Macroscopic fossils from all major lineages of land plants are found from about 416 to
359 mya.
b. Most structural adaptations to terrestrial life appeared: vascular tissue and roots.
C. Plants probably colonized land with the assistance of fungi.
4. The Carboniferous period
a. Extensive coal deposits formed between 359 and 299 mya.
b. Most of the coal was formed from club mosses, horsetails, and ferns.
5. Diversification of gymnosperms
a. Gymnosperms are prominent in the fossil record from 299 to 145 mya.
b. Gymnosperms grow well in dry habitats, so plants probably colonized drier
environments during this time.
6. Diversification of angiosperms
a. Fossil angiosperms appeared about 150 mya and are still dominant today.
7. Summary of the fossil record: The green algae appear first, followed by the nonvascular
plants, seedless vascular plants, and seed plants. Organisms that appear late in the fossil record
are much less dependent on water than groups that appear earlier.
C. Evaluating molecular phylogenies (Fig. 28.6)
1. The current molecular phylogenetic tree suggests these interpretations:
a. The green algal group Zygnematophyceae is the closest living relative to land plants.
b. Nonvascular plants are the most ancient living group of land plants.
c. Monophyletic groups are: green plants, land plants, vascular plants, seed plants,
gymnosperms, and angiosperms.
d. Paraphyletic groups are: green algae, nonvascular plants, and seedless vascular plants.
2. Students should be able to explain how morphological data, the fossil record, and molecular
phylogenies all support the hypothesis that land plants evolved from green algae.

28.3 What Themes Occur in the Diversification of Land Plants?

● Compare and contrast the life cycles and key traits of green algae, nonvascular plants, seedless
vascular plants, gymnosperms, and angiosperms.
● Explain the adaptations that allowed plants to live on land.
● Map evolutionary changes on the land plant phylogeny.
● Apply the alternation of generations to the major groups of plants.
 ● Describe key features of the major lineages of green algae and land plants.

28.3 What Themes Occur in the Diversification of Land Plants?

A. The transition to land, I: How did plants adapt to dry conditions with intense sunlight?
1. Terrestrial habitats have more sunlight and more CO2 than aquatic habitats.
● Advantages:
○ Sunlight is abundant
○ CO2 readily available (diffuses faster in air)
○ Dry land has no predators
● Disadvantages:
○ Avoid drying out (water loss)
○ Disperse reproductive cells in the air
○ Structural support (overcome gravity)
○ Exchange gasses without water
○ Move molecules with bulk flow (as size increases)
○ Exposure to UV radiation (adaptation was the same as for water loss)
2. Preventing water loss:
a. Cuticle: waxy sealant that prevents the loss of H2O but also inhibits the uptake of
CO2. (Fig. 28.7a)
b. Stomata pores bounded by guard cells that allow the uptake of CO2 while controlling
water loss. (Fig. 28.7b)
c. Liverworts have simple pores; all other land plants today have stomata.
3. Providing protection from UV irradiation (similar to water loss adaptation)
a. Early plants contained compounds that could absorb damaging UV light.
4. The importance of upright growth
a. Early plants probably had a low, sprawling growth habit.
b. Advantages: Plants capable of vertical growth would have an advantage in competing
for space and light
c. Disadvantages: (1) transporting water up the plant from the soil (2) becoming rigid
enough to withstand wind and gravity.
5. The origin of vascular tissue (solution for upright growth)
a. Fossilized plants dated to 400 mya had elongated cells containing lignin that were
probably vascular tissue. (Fig. 28.8a, b)
6. Elaboration of vascular tissue: tracheids and vessels
a. Tracheids have long, thin tapered ends, with lignin rings in secondary cell walls for
support. Water flows through pits in secondary cell walls. Tracheids first appear in fossils
dated to 380 mya. (Fig. 28.8c)
b. Vessel elements are shorter and stacked end to end like a pipe. Water flows through
perforations that completely lack cell-wall material. Vessels first appear in fossils dated
to 250 to 270 mya. (Fig. 31.8d)
c. Both tracheids and vessel elements are dead and lack cytoplasm at maturity.
B. Mapping evolutionary changes on the phylogenetic tree (Fig. 28.9)
1. Fundamentally important adaptations to dry conditions—such as the cuticle, pores, stomata,
vascular tissue, and tracheids—evolved only once.
2. Water-conducting cells evolved independently in mosses and vascular plants.
3. Vessels evolved independently in gnetophytes and angiosperms.
C. The transition to land, II: How do plants reproduce in dry conditions?
1. Desiccation-resistant sporopollenin-encased spores were one of the first innovations making
the colonization of land possible.
2. Protective, complex reproductive organs
a. The evolution of an elaborate gametangium protected gametes from drying and from
mechanical damage.
b. There are two types of gametangia: Antheridia produce sperm, and archegonia
produce eggs. (Fig. 28.10)
3. Embryos nourished by parental tissues
a. Land plants retain their eggs in the archegonia. Once fertilized, the zygote begins to
develop on the parent plant and receives nutrients from it.
b. For this reason, plants are called embryophytes.
4. Alternation of generations
a. In conjugating algae, coleochaetales, and stoneworts, the multicellular form is
haploid; the only diploid form is the zygote. (Fig. 28.11)
b. Plants alternate between a multicellular haploid stage and a multicellular diploid
stage. (Fig. 28.12)
(1) The diploid sporophyte produces haploid spores by meiosis.
(2) A spore grows via mitosis to become a new gametophyte.
(3) A haploid, multicellular form called the gametophyte produces haploid
gametes via mitosis.
(4) Two gametes fuse to form a diploid zygote.
(5) The zygote grows via mitosis to become the diploid multicellular form, called
the sporophyte.
c. Alternation of generations is a difficult topic to master—compare and contrast the
lifecycle of land plants with that of green algae. (Making Models 28.1)
d. Concept check: You should be able to summarize the sequence of events in a lifecycle
with alternation of generations starting with a sporophyte.
5. From gametophyte-dominant to sporophyte-dominant
a. In nonvascular plants, the dominant form is the haploid gametophyte. (Fig. 28.13)
b. In ferns, the diploid sporophyte is larger. (Fig. 28.14)
c. In gymnosperms and angiosperms, the sporophyte is dominant and the microscopic
gametophyte is retained within the sporophyte.
d. The transition from gametophyte-dominated lifecycles to sporophyte-dominated
lifecycles is one of the most striking trends in land plant evolution and includes the
continued reduction of the gametophyte (Fig 28.15).
e. Students should be able to examine the photos of hornworts (a nonvascular plant)
and horsetails (a seedless vascular plant) in Figure 28.15 and identify which is the
gametophyte and which is the sporophyte.
6. Heterospory
a. All nonvascular plants and most seedless vascular plants are homosporous, meaning
they produce a single type of spore. (Fig. 28.16a)
b. Seed plants are heterosporous, with two distinct spore-producing structures that
produce two types of spores. (Fig. 28.16b)
(1) Microsporangia make microspores. Microspores grow to become male
gametophytes, which produce the sperm.
(2) Megasporangia make megaspores. Megaspores grow to become female
gametophytes, which produce the eggs.
(3) The gametophytes of seed plants are either male or female, but never both.
 7. Pollen
a. A pollen grain is a tiny male gametophyte surrounded by a tough coat of
sporopollenin.
b. When pollen evolved, heterosporous plants no longer needed water to accomplish
fertilization. Instead of swimming to the egg as a naked sperm cell, the tiny male
gametophytes took to the skies.
8. Seeds
a. A seed includes an embryo and a food supply surrounded by a tough coat.
b. Seeds enable embryos to be dispersed to new habitats. (Fig. 28.17)
c. A summary of the traits of seed plants can be seen in the lifecycle of a pine tree. (Fig.
28.18)
9. Flowers
a. Flowering plants (angiosperms) are the most successful land plants.
b. Flowers contain two reproductive structures: stamens and carpels. (Fig. 28.19)
(1) Stamens have anthers, which contain the microsporangia.
(2) Carpels have ovaries, containing ovules, which contain the megasporangia.
(i) The evolution of the ovary was a key innovation that protects female
gametophytes from insects and other predators.
c. In double fertilization, a pollen grain produces two sperm cells. One sperm cell fuses
with the egg to form an embryo. The other sperm cell fuses with two nuclei in the
female gametophyte to form triploid endosperm.
(1) The adaptive significance of double fertilization is still not understood.
10. Pollination by insects and other animals
a. Sepals and petals enclose the ovary and give flowers a wide variety of colors, shapes,
and smells.
b. Directed-pollination hypothesis: Flowers are an adaptation to attract specific
pollinators (rather than leaving pollination to the wind), thus increasing the probability
that pollination will occur.
c. Evidence for this hypothesis: The characteristics of a flower (scent, flower shape,
color, etc.) correlate with the characteristics of its pollinator.
(1) Examples: carrion flowers, hummingbird-pollinated flowers, bee-pollinated
flowers (Fig. 28.20)
d. Experimental evidence: flower color in South American petunias
(1) Flowers with genetically altered flowers were visited differently by different
pollinators. (Fig. 28.21)
(2) Conclusion: Flower color is an adaptation that determines the type of
pollinator visiting the flower.
11. Fruits
a. A fruit is a structure derived from the ovary and encloses one or more seeds. (Fig.
28.22a)
b. A fruit is an adaptation for seed dispersal. Fruit tissues are nutritious and attractive, so
animals eat the fruit and disperse the seeds via their feces. (Fig. 28.22b)
12. Summary: Once land plants could grow efficiently in dry habitats, traits associated with
pollination and seed dispersal drove further diversification. (Fig. 28.23)
D. The angiosperm radiation
1. The Anthophyta (angiosperms, flowering plants) represent one of the significant adaptive
radiations in evolutionary history.
2. Angiosperms were traditionally divided into monocots and dicots. (Fig. 28.24)
 a. Monocots have one cotyledon (embryonic leaf). Examples: grasses, orchids, palms,
lilies
b. Dicots have two cotyledons. Examples: roses, daisies, maples
3. Genetic analysis has shown that monocots are monophyletic but dicots are not. (Fig. 28.25)
a. The term eudicot is now used for the monophyletic group that includes roses, daisies,
and maples.

Alternating Generation Life Cycle

● Color change = fertilization (n -> 2n) / meiosis (2n -> n)
● Red = diploid, blue = haploid
● Mitosis when no ploidy change
● Gametophyte = multicellular haploid phase
● Sporophyte = multicellular diploid phase
● Gametes -> Fertilization -> Zygote -> Mitosis -> Sporophyte -> Meiosis -> spores -> Mitosis ->
gametophyte -> Gametes

29.3 What Themes Occur in the Diversification of Fungi?

● Summarize the types of symbiotic relationships that fungi can have with other organisms.
● Describe the symbiotic relationship between fungi and land plant species.
● Compare and contrast the life cycles and mode of nutrition among fungi, animals and plants.
● Explain the adaptations making fungi effective as decomposers.
● Explain the variation in reproductive strategies of fungi.
● Describe the four fundamental types of fungal life cycles.

In-Class Notes
● chitin cell wall
● flagella: single, found in zoospores (gametes), and move in whiplike manner
● yeast = single celled fungi
● mycelia = multicellular weblike network of very thin hyphae
○ PRO: Highest surface area to volume ratio of all multicellular organisms -> efficient
nutrient absorption
○ CON: Prone to dry out (found mostly in moist environments), but reproductive spores
are resistant to drying out during dry periods and then germinate
● Reproductive Structures
○ Swimming gametes and spores
○ Zygosporangia: spore producing structures formed when hyphae are yoked
○ Basidia: club shaped cells where meiosis occurs, forming 4 spores
○ Asci: sac like cells where meiosis and one round of mitosis occur, forming 8 spores
■ Similar to Basidia but with a long line of cells

A. Fungi often participate in symbioses.

1. Mutualistic relationships benefit both species, parasitic relationships benefit one species at
the expense of the other, and commensal relationships benefit one species with no effect on the
other.
3. Ectomycorrhizal fungi (EMF) (Fig. 29.12a)
a. EMF are often basidiomycetes (or occasionally ascomycetes).
 b. They form a dense network of hyphae (0.1 mm thick) around plant roots, extending
between root cells and into the soil.
4. Arbuscular mycorrhizal fungi (AMF; endomycorrhizal fungi) (Fig. 29.12b)
a. AMF are members of Glomeromycota.
b. Highly branched hyphae penetrate the cell walls of root cells and contact the plasma
membrane directly. This increases the contact area for the exchange of molecules.
d. They deliver phosphorus to plants but not nitrogen.
5. Endophytes
a. Endophytes are fungi that live in the above ground tissues of a plant.
b. Some may be beneficial. For example, endophytes in some grasses and in morning
glories produce compounds that deter herbivores.
c. Others may be commensals since some studies have not documented any benefit to
the host plant.
6. Other symbioses
B. What adaptations make fungi such effective decomposers?
1. Extracellular digestion
2. Lignin degradation
3. Cellulose digestion
C. Variation in reproduction
1. Spores as key reproductive cells
a. Spores are the dispersal stage in the fungal lifecycle.
b. Spores are produced both by asexual and sexual reproduction.
c. If food becomes scarce, a mycelium responds by forming spores that can be
dispersed by water, wind, or animals.
d. If a spore falls on a food source, it germinates and forms a new mycelium.
2. Multiple mating types
a. Many fungi have mating types (analogous to sexes) that look identical. For example,
zygomycete hyphae fuse and reproduce only if they carry alleles from different mating
types.
b. Instead of having just two sexes, a single fungal species may have tens of
thousands.
3. How does fertilization occur?
a. Chytrids are the only fungi that produce gametes, and they are not different enough in
size to be called sperm and egg.
b. Fertilization in other fungi occurs in two distinct steps: (Fig. 29.15) Compare and
contrast these events with the lifecycles of other eukaryotes.
(1) Plasmogamy: The cytoplasm from different cells fuses. The nuclei may
remain independent; that is, the mycelium is heterokaryotic.
(2) Karyogamy: Eventually, a pair of unlike nuclei fuse to form a diploid zygote.
The fused nucleus then divides by meiosis to form spores.
4. Asexual reproduction
a. Many fungi reproduce asexually. (Fig. 29.15 left)
b. Spore-forming structures are produced by a haploid mycelium.
E. Four major types of lifecycles (compare and contras t)
1. Chytrid lifecycle (Fig. 29.16a)
2. Zygomycete lifecycle (Fig. 29.16b)
3. Basidiomycota lifecycle (Fig. 29.16c)
4. Ascomycota lifecycle (Fig. 29.16d)
Introduction Chapter 29
● Summarize the important roles fungi play in the environment.
● Explain the economic impact of fungi.
● Explain the ecological impact of fungi.
● Describe the relationship between mycorrhizal fungi and land plants.
● Explain the impact of saprophytic fungi on the carbon cycle.

A. What are the fungi?

1. Fungi are one of the three major lineages of multicellular eukaryotes.
2. Fungi absorb carbon and energy from other organisms.
3. Fungi may be decomposers or parasitic or beneficial symbiotes.
4. Fungi play a key role in nutrient cycling in terrestrial ecosystems.
5. Fungi serve in mutualisms which are critical for life on Earth, such as mycorrhizal associations
with land plants.

In-Class Notes
Fungi Mutualism
1. Mychorrhizae: fungal mycelium underground with plant root (no sexual reproduction)
● Fungi -> water and nutrients -> Plants -> carbohydrates -> Fungi
● Found on 80-90% of plants
● Types
○ Ectomycorrhizal fungi (EMF): around roots and between root cells; forms dense,
continuous sheath around root (mostly in temperate and boreal forests)
1. EX1. Sheath protects from heavy metal contamination
2. EX2. Cleracut logging/Wildfires: remaining trees provide inoculum for
new seedings (soil transfer from mature to new area
○ Arbuscular mycorrhizal fungi (AMF): penetrate cell wall and contacts plasma
membrane (mostly in tropical regions)
2. Endophytes: live between and within plant cells (in roots and above tissue)
● Benefits: Increase drought tolerance, produce pesticide toxins
3. Lichens: between fungus and either photosynthetic bacterium or alga (on tree or another plant)
● Algae -> provide photosynthetic food -> Lichen -> protection + nutrients -> Algae

Lifecycle
● Asexual:
● Sexual: zygote (2n) -> meiosis -> spore producing structure (n) -> mitosis -> spores (n) -> mitosis
-> mycelium (n) -> plasmogamy -> heteokaryotic mycelium (n+n) -> mitosis -> karyogamy ->
zygote
● (Blue n -> Black n) Plasmogamy: fusion of cytoplasm from two individuals
● (Black n -> Red 2n) Karyogamy: fusion of the nuclei from two individuals to form diploid zygote
● (Black - n+n: 2 haploid nuclei) Heterokaryotic VS. (Red - 2n) Diploid VS. (Blue - n) Haploid
● Differences
○ Spores can be produced by BOTH meiosis and mitosis (in asexual)
● Reproductive structures
○ Swimming gametes and spores
○ Zygosporangia: spore producing structures formed when hyphae are yoked
○ Basidia: club shaped cells hen meiosis occurs, forming 4 spores
 ○ Asci: sac-like cells where meiosis and one round of mitosis occur -> form 8 spores

29.1 Why Do Biologists Study Fungi?

A. Fungi have important economic and ecological impacts.
1. No more than 300 species of fungi cause human disease. Examples: athlete’s foot, diaper rash,
vaginitis, pneumonia, thrush
2. Soil-dwelling fungi have been the source of many important antibiotics.
3. Certain fungi destroy billions of dollars of crops each year. (Fig. 29.1)
4. Many fungi are used to make food.
a. Mushrooms are a popular edible fungus.
b. Yeasts are used to make bread, beer, wine, and other foods.
c. Chocolate is made from the seeds of plants fermented by fungi.
d. Enzymes derived from fungi improve the characteristics of several foods.
5. Fungi have destroyed significant numbers of trees in North America. Examples: chestnut
blight, Dutch elm disease
B. Mycorrhizal fungi provide nutrients for land plants.
1. Mycorrhizal fungi are fungi that live in close association with plant roots.
2. The fungi provide the plant with water and key nutrients, such as nitrogen and phosphorus, in
exchange for sugars.
3. Without these fungi, plant growth is greatly slowed; therefore, these fungi are important to
agricultural productivity. (Fig. 29.2)
C. Saprophytic fungi accelerate the carbon cycle on land. (Fig. 29.3)
1. Carbon cycling during the Carboniferous period
a. The coal deposits of the Carboniferous may be the result of a scarcity of saprophytic
(decomposing) fungi at the time.
b. The lack of fungi allowed large deposits of dead plant tissue to build up, eventually
producing coal.
c. Biologists hypothesize that because peatlands have an acidic pH, the fungi could not
grow in them.
2. Carbon cycling at the end-Permian
a. A “fungal spike” (a large increase in fungal fossils) coincides with the end-Permian
mass extinction.
b. The end-Permian extinction may have involved a massive die-off of land plants,
resulting in a population explosion of saprophytic fungi.
3. Carbon cycling at present
a. Today, saprophytic fungi speed the terrestrial carbon cycle.
b. Fungi are almost the only organisms capable of digesting both cellulose and lignin,
recycling carbon into glucose and carbon dioxide.
c. Without fungi, carbon would be trapped in the wood for a very long time, and
terrestrial environments would be far less productive.
4. Concept check: You should be able to explain how fungi help connect two major parts of the
the cycle: carbon fixation and carbon release.

29.2 How Do Biologists Study Fungi?

● Analyze key features used to study fungi.
 ● Describe the key morphological traits that distinguish the major groups of fungi.
● Evaluate the molecular phylogeny of fungi.

A. About 110,000 species of fungi have been described.

1. A Panama study found that the leaves of just two tree species housed 418 fungal species.
2. A direct sequencing study found that more than 650 species of fungi (200 previously
unknown) were found in the guts of 27 species of beetles.
B. Analyzing morphological traits
1. Fungi have only two growth forms:
a. Single-celled yeasts (Fig. 29.4a)
b. Multicellular, filamentous mycelia (Fig. 29.4b)
2. The nature of the fungal mycelium
a. Mycelia can be very long-lived and very large.
b. Mycelia constantly grow in the direction of food sources and die back when food is
scarce.
c. Mycelia are made up of individual filaments called hyphae.
3. The nature of hyphae
a. A hypha may have just one haploid nucleus or several (heterokaryotic). Most
heterokaryotic hyphae are dikaryotic (two nuclei per cell, one from each parent).
b. A hypha is a long, narrow filament that branches frequently. (Fig. 29.5a)
c. Each hypha is subdivided by septa (walls) with pores through which cytoplasm,
organelles, and other material can flow. Due to this flow, a fungal mycelium is
intermediate between a multicellular organism and a large unicellular organism. (Fig.
32.5b)
d. Coenocytic fungi have hundreds or thousands of nuclei scattered throughout the
mycelium. (Fig. 29.5c)
e. Some fungi produce hyphae for prey capture and nutrient uptake. (Fig. 29.6)
4. Mycelia have a large surface area.
a. The shape of mycelia gives fungi the highest surface-area-to-volume ratio of all
multicellular organisms.
b. The large surface area is important because fungi make their living via absorption;
however, it also makes fungi susceptible to dying out.
c. When conditions dry, fungal mycelium may die back partially or completely. Spores
may may also be produced.
5. Reproductive structures
a. Chytrids have swimming gametes and spores. (Fig. 29.7a)
b. Zygomycetes produce a distinctive spore-producing structure called a
zygosporangium, which develops when haploid hyphae from two individuals meet. (Fig.
29.7b)
c. Basidiomycetes (mushrooms, puffballs, etc.) form spores in small pedestal-like
structures called basidia at the ends of hyphae. (Fig. 29.7c)
● Diploid sporophyte
● No assexual reproduction (or at least not very common)
● 4 spores released
d. Ascomycetes produce spores with specialized cells called asci. (Fig. 29.7d)
● “Sack” fungi
● Extra step (before spores are released)
 ○ Instead of dispersal of spores immediately after meiosis, there is an
extra mitosis step (i.e. 8 spores released instead of 4)
e. Many fungi are quite good at asexual reproduction as well as sexual reproduction.
Some produce trillions of asexual spores called conidia. (Fig. 29.8)
NOTE: Yeast produced by budding (starts off small and then gets bigger as it punches off)
C. Evaluating molecular phylogenies
1. Fungi are closely related to animals. (Fig. 29.9)
a. Animals and fungi both produce chitin (in cell walls), have similar flagella (in spores
and gametes), and use glycogen to store energy.
2. What are the relationships among the major fungal groups? (Fig. 29.10)
a. Microsporidians are actually fungi (disease causing parasites)
b. Chytrids and zygomycetes form a paraphyletic group that is poorly resolved (difficult
to discern).
● Chytrid: (1) only fungi that produce motile cells
○ many decompose plants by digesting cellulose (ex. Mutualism in guts of
mammals)
○ parasitism in freshwater species
○ Degrades animals water permeable skin (swimming spores spread
easily)
c. A group called the Glomeromycota are monophyletic.
d. Basidiomycota and Ascomycota are each monophyletic groups, and together they
form a monophyletic group.
e. The sister group to fungi consists of choanoflagellates (protists) and animals

29.3 What Themes Occur in the Diversification of Fungi?

● Summarize the types of symbiotic relationships that fungi can have with other organisms.
● Describe the symbiotic relationship between fungi and land plant species.
● Compare and contrast the life cycles and mode of nutrition among fungi, animals and plants.
● Explain the adaptations making fungi effective as decomposers.
● Explain the variation in reproductive strategies of fungi.
● Describe the four fundamental types of fungal life cycles.

A. Fungi often participate in symbioses.

1. Mutualistic relationships benefit both species, parasitic relationships benefit one species at
the expense of the other, and commensal relationships benefit one species with no effect on the
other.
3. Ectomycorrhizal fungi (EMF) (Fig. 29.12a)
a. EMF are often basidiomycetes (or occasionally ascomycetes).
b. They form a dense network of hyphae (0.1 mm thick) around plant roots, extending
between root cells and into the soil.
4. Arbuscular mycorrhizal fungi (AMF; endomycorrhizal fungi) (Fig. 29.12b)
a. AMF are members of Glomeromycota.
b. Highly branched hyphae penetrate the cell walls of root cells and contact the plasma
membrane directly. This increases the contact area for the exchange of molecules.
d. They deliver phosphorus to plants but not nitrogen.
5. Endophytes
a. Endophytes are fungi that live in the above ground tissues of a plant.
 b. Some may be beneficial. For example, endophytes in some grasses and in morning
glories produce compounds that deter herbivores.
c. Others may be commensals since some studies have not documented any benefit to
the host plant.
6. Other symbioses
B. What adaptations make fungi such effective decomposers?
1. Extracellular digestion
2. Lignin degradation
3. Cellulose digestion
C. Variation in reproduction
1. Spores as key reproductive cells
a. Spores are the dispersal stage in the fungal lifecycle.
b. Spores are produced both by asexual and sexual reproduction.
c. If food becomes scarce, a mycelium responds by forming spores that can be
dispersed by water, wind, or animals.
d. If a spore falls on a food source, it germinates and forms a new mycelium.
2. Multiple mating types
a. Many fungi have mating types (analogous to sexes) that look identical. For example,
zygomycete hyphae fuse and reproduce only if they carry alleles from different mating
types.
b. Instead of having just two sexes, a single fungal species may have tens of
thousands.
3. How does fertilization occur?
a. Chytrids are the only fungi that produce gametes, and they are not different enough in
size to be called sperm and egg.
b. Fertilization in other fungi occurs in two distinct steps: (Fig. 29.15) Compare and
contrast these events with the lifecycles of other eukaryotes.
(1) Plasmogamy: The cytoplasm from different cells fuses. The nuclei may
remain independent; that is, the mycelium is heterokaryotic.
(2) Karyogamy: Eventually, a pair of unlike nuclei fuse to form a diploid zygote.
The fused nucleus then divides by meiosis to form spores.
4. Asexual reproduction
a. Many fungi reproduce asexually. (Fig. 29.15 left)
b. Spore-forming structures are produced by a haploid mycelium.
E. Four major types of lifecycles (compare and contrast)
1. Chytrid lifecycle (Fig. 29.16a)
● Alternation of generation
2. Zygomycete lifecycle (Fig. 29.16b)
● No alternation of generations
● Meiosis immediately after karyogamy
● No gametophyte
● Haploid sporophyte
● Yolking of hyphae
3. Basidiomycota lifecycle (Fig. 29.16c)
4. Ascomycota lifecycle (Fig. 29.16d)

coe
Features of Animals
● Multicellular eukaryotic organisms
○ Extensive extracellular matrix (for communication)
● Heterotrophic (does not generate its own food source)
● Can move under own power at some point in life cycle (ex. gametes)
● (Except for sponges) have neurons that transmit electrical signals and muscle cells that shape the
body

Origin
● Mostly close related to choanoflagellate protists (single celled, sessile protists, some are
colonial) -> direct water current using flagella
● Compare to sponge
● Lophotrochozoans
● Coelomates

Features used to classify animals

1. Body symmetry
a. Radial: (1) generates identifcal body halves around a central axis (2) development of a
head if rare (3) best suited for a sessile lifestyle
i. Secondary radial symmetry: larvae have bilateral symmetry and adults have
radial symmetry
b. Bilateral: (1) generate left and right halves along a sagittal plane (2) allows for directional
movement + cephalization
2. Embryological development: zygote -> cleavage -> eight cell stage -> cleavage -> blastula cross
section -> gastrulation -> gastrula cross section (with blastopore: mouth or anus)
a. Number of germ layers (triploblast vs diploblastic)
b. Presence or absence of coelom
c. Embryonic development of a mouth

Phylum Porifera
● Lack organ systems and no tissue level organization: specialized cells for feeding, reproduction,
support, etc.
● Digestion: food ingested and digested by individual cells
○ Benthic (bottom of the ocean) and sessile -> dispersal by ciliated larvae
○ Feeding type: most are suspension feeders some photosynthetic symbionts
■ Feeding cells captures bacteria and other food particles in water currents and
closely resemble choanoflagellates
● Structure: made of spicules (made of strong calcium carbonate or silica) that provide structural
support to extracellular matrix
● Reproduction:
○ Assexual: mitosis, fission, fragmentation, budding or gemmules (offspring are clones)
○ Sexual - monoecious: has both male and female reproductive organs at the same time
■ Requires meiosis and fusion of haploid gametes
■ Internal fertilization: gametes from one individual to go inside of another
individual and find gametes
■ External fertilization:
■ Parthenoengisis: vrgin beginning where males develop (FINISH THIS)
○ Where do embryos develop
 ■ Viviparous: inside mother where mom had a physiological connection with
embryo for nutrient exchange
■ Oviparous: eggs (with nutrients for embryo)
■ Ovoviviparous: eggs stay inside mother (snakes, sharks, fish, seahorse)
○
● Suspension feeders: capture food by filtering particles drifting in waters

● FINISH THIS

Phylum Cnidaria
● Diploblasts
● Radial symmetry
● Two distinct body plans: medusa (jellyfish) vs polyp
● FINISH THIS
● Asexual reproduction: budding
● Cnidocytes & Nematocysts:
○ Stinging cells
○ Present around mouth and tentacles
○ Fired in response to touch
○ Coiled threads release toxins

Hydrostatic Skeletons
●
●

Movement
● Function of animal locomotion: finding food, finding mates, escaping from predators, dispersing
to new habitats
● Three types of skeletal systems that enable complex movements
○ Endoskeletons: derive support from rigid structures inside the body
○ Exoskeletons: derive support from rigid structures outside the body (ex. insects)
○ Hydrostatic skeletons: support from flexible body wall in tension surrounding fluid or
soft tissue under compression
■ Support2 from flexible body wall surrounding fluid or soft tissue
■ Tension in the body wall compressed fluid
■ Prevents collapse of body
■ Muscles work against fluid to create movement

Phylum Ctenophora
● Diploblasts
● Biradial symmetry
● Monoecious
● Planktonic and predatory
○ No stringing cells -> sticky cells tot trap prey

● Protostomes: spiral cleavage + blastula developed into mouth (hole on the bottom)
● Deuterostomes: radial cleavage + blastula developed into anus
○ Both are monophyletic
 ● Supherphylium Lohotrochozoea: annelids, molluscs, platyhelminthes
○ Has either a lophophore (ciliated horse-shoe feeding shaped structure - filter feeding) or
a trochophore (free swimming, planktonic marine larval stage - ring of cilia around their
middle that functions in seeping and sometimes in feeding)
● Superphylum Ecdysozoa: Nematoda, Arthropoda
○ Has cuticle (tough, flexible exoskeleton that protects animal from water loss, predators,
external environment)
○ All most at least once in their lifetime
■ Ecdysis: process of molting and secreting new cuticle
○ Metamorphosis: process of transformation in appearance from an immature form to an
adult form in two or more distinct stages
■ Complete: drammatic stage with a pupa/chrysalis
■ Incomplete: increases in size with each shedding (5 instars)

Introduction & 30.1 What is an Animal?

● Analyze the characteristics that distinguish animals from other organisms.
● Describe the defining characteristics of animals.
● Compare animals to plants and fungi.
● Describe the significance of the Cambrian explosion.
● List some of the major lineages of animals.

Introduction
- The common ancestor of animals lived about 800 million years ago.
- There are an estimated 3 to 10 million animal species alive, although only 1.4 million have been
described.

I. What Is an animal?
A. Animals occur in a clade called Opisthokonta. (Fig. 30.1)
B. Animals share these key traits:
1. They are multicellular eukaryotes that move under their own power.
2. Outside of sponges, they all have both nerve and muscle cells.
3. Animals are the only multicellular heterotrophs that ingest their food prior to
digesting it.
4. They are the largest predators, herbivores, and detritivores.
C. There are 30 to 35 recognized phyla. (Table 30.1)
D. The radiation of animals began about 550 million years ago during the Cambrian Explosion.

30.2 What Key Innovations Occurred during the Origin of Animal Phyla?
● Analyze the significance of the origin of key innovations during the early radiation of animals.
● Describe the types of data biologists can use to study the early evolution of animals.
● Explain the significance of the origin of multicellularity in animals.
● Explain the significance of the origin of embryonic tissue layers in animals.
● Explain the significance of the origin of muscle cells in animals.
● Explain the significance of the origin of body symmetry in animals.
● Explain the significance of the origin of the nervous system in animals.
● Explain the significance of the origin of the head in animals.
 ● Explain the significance of the origin of the gut in animals.
● Explain the significance of the origin of the coelom in animals.
● Describe the major non-bilaterian taxa.
● Describe which major taxa belong in the Protostomes.
● Describe which major taxa belong in the Deuterostomes.
● Explain the significance of the origin of segmentation in animals.
● Explain why the evolution of animal phyla was not a smooth transition from simple to complex.

II. What Key Innovations Occurred during the Origin of Animal Phyla?
A. There are several sources of data that suggest the same evolutionary sequence. (Fig. 30.2)
1. Fossils provide direct evidence of past forms but are incomplete in their coverage of the
history of life.
2. Comparative morphology provides information about which embryonic, larval, or adult
morphological characteristics are common and which are unique to particular lineages.
3. Comparative development provides information about patterns of gene expression and
morphological change during development.
4. Comparative genomics provides information about the relative similarity of genes or whole
genomes of diverse organisms.
B. Origin of multicellularity Read through this section, but you will not be assessed on it.
1. Fossil evidence—Sponges appear in the record more than 700 mya.
2. Morphological evidence—Choanocytes and sponge-feeding cells are almost identical in
structure and function. (Fig. 30.3)
3. Molecular evidence—Sponges are paraphyletic, providing support of a sponge-like common
ancestor to all animals.
a. All possess a complex developmental tool kit of genes, suggesting a series of important
genetic innovations that occur at the root of the animal tree along with multicellularity.
4. Alternative views: The Ctenophores-first hypothesis
a. This hypothesis is based on the pattern of gains and losses of certain genes in the
ctenophores. There is not enough evidence to reject this hypothesis.
5. Insights from the origin-of-animals debate
a. The evolution of animals is more complicated than a smooth transition from simple to
complex.
b. Many key innovations did not arise all at once.
c. Evolution did not stop within any of the lineages. (Making Models 30.1)
C. Origin of embryonic tissue layers
1. All animals have tissues, which are groups of similar cells organized into structural and
functional units.
2. All other animals have at least two different types of tissues that are derived from germ layers,
which are tissue layers in the embryo.
a. There are three germ layers:
(1) Endoderm gives rise to the lining of the digestive tract.
(2) Ectoderm gives rise to the skin and nervous system.
(3) Mesoderm gives rise to the circulatory system, muscles, and internal
structures such as bone and most organs.
b. Diploblasts have two germ layers: ectoderm and endoderm. (Fig. 30.4) (BioSkills 15)
c. Triploblasts have three germ layers: ectoderm, endoderm, and mesoderm.
d. All animals share homologous genes for contractile proteins.
D. Origin of bilateral symmetry, cephalization, and the nervous system
 1. Body symmetry is a key morphological aspect of an animal’s body plan.
a. Ctenophores, many cnidarians, and some sponges have radial symmetry. (Fig. 30.5a)
b. Bilaterally symmetric animals have only a single plane of symmetry. (Fig. 30.5b)
2. Homology or convergent evolution?
a. Cnidarians that appear to be radially symmetric can be seen to actually have bilateral
symmetry upon closer inspection. (Fig. 30.6)
b. Bilateral symmetry is achieved by the combination of the two genes responsible for
anterior–posterior and dorsal–ventral axes formation.
c. The Hox and dpp genes in Nematostella is homologous to bilaterians. (Fig. 30.7)
3. Origin of the nervous system
a. Sponges have no neurons, no well-defined symmetry, and no head region.
b. Cnidarians and ctenophores have a nerve net and radial symmetry but no head
region. (Fig. 30.8a)
(1) These animals are equally likely to encounter prey and other environmental
stimuli from any direction.
c. All other animals (i.e., the triploblasts) have bilateral symmetry, a head region, and a
central nervous system (CNS) with ganglia. (Fig. 30.8b)
(1) They tend to move in one direction and thus to encounter environmental
stimuli at only one end.
(2) Evolution of bilateral symmetry is associated with cephalization: evolution of
a head region that contains sensing, feeding, and information-processing
structures such as eyes, mouth, and brain.
(3) This is an efficient design for directed movement, hunting, and capturing
food.
E. Origin of the coelom
1. The basic bilaterian body shape is a tube within a tube. (Fig. 30.9)
2. Many triploblasts have a fluid-filled internal cavity called a coelom. (Fig 30.10)
3. Molecular data suggest that some lineages (such as flatworm ancestors) had a coelom, but
then those traits were lost.
F. Origin of protostomes and deuterostomes
1. Bilaterians (triploblastic, bilaterally symmetric animals) can be split into two subgroups:
protostomes and deuterostomes.
2. Protostome development
a. The mouth forms first during gastrulation.
b. The coelom forms via splitting of blocks of mesoderm.
3. Deuterostome development
a. The anus forms first during gastrulation.
b. The coelom forms via mesoderm pinching off from the gut.
4. These represent two ways of achieving the same end—a bilaterally symmetric body that
contains a cavity lined with mesoderm.
5. There are two major groups within the protostomes:
a. Lophotrochozoa—include the mollusks, annelids, flatworms, and rotifers
b. Ecdysozoa—include the arthropods and nematodes
G. Origin of segmentation
1. Segmentation is the presence of repeated body structures.
2. Is segmentation an example of convergent evolution?
● Survivorship Curves
○ NOTE: number of survivors in log scale
○ Type I (EX. humans): high survivorship at young age (not equal probability of dying as
age increases) →
■ Heavy parental investment (therefore, not too many offspring) + most
individuals approach max lifespan
○ Type II (EX. birds): steady survivorship
■ Parental care early in life + Vulnerable to mortality at any age
○ Type III (EX. octopus): Very high morality at young ages + high survival at older ages +
have plenty of available nutrients (lots of eggs produced)

○
● Fecundity: the average number of female offspring produced per female in the population over
some period of time
● R0 > 1 => Population is increasing
● R0 = 1 => Population is stable