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Exam 2 Study Guide
Chapters 8-14
Chapter 8: From Single-Celled
Organisms to Kingdoms
Aristotle
(384-322 BCE)
Greek
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Two kingdom system: Plantae and
Animalia; This classification lasted
for more than 2000 years
His writings cover many subjects,
including physics, metaphysics,
poetry, theater, music, logic,
rhetoric, linguistics, politics,
government, ethics, biology, and
zoology.
He was a student of Plato and a
great mind of the time, but his
legacy as an unquestioned
authority held back scientific
progress for centuries.
He made collections of creatures,
did dissections of animals,
recognized different kinds of
organisms.
He noted the sequence of organ
development by observing
chicken eggs.
The world can be understood with
observation and reason
a slow rate for geological change,
undetectable in the lifetime of a
human being
proclaimed that there was a
hierarchical order of species from
most imperfect to most perfect, a
concept refined over the centuries
Carl von Linné
(Carolus
Linnaeus)
(1707-1778)
Swedish
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Three Kingdoms
with Protistans
Richard Owen
(1804-1892)
British
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Charles Darwin
(1809-1882)
English
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as the "Great Chain of Being."
Scala Naturae (Scale of Nature)
which ranked things from the
inorganic to humans to Gods.
believed species were immutable
1735- three kingdom system:
Plantae (L. planta, plant), Animalia
(L. anima, breath, life), and
Lapideum (L., lapedeus, stone)
Popularized the binomial
nomenclature
The idea originated with Swiss
Botanist Gaspard Bauhin in 1623 in
his Pinax Theatri Botanici
Attempted to classify the material
world as evidence of the power of
the Christian God with Systema
Naturae (1753)
John Hogg (1800-1869)
Sir Richard Owen (1804-1892)
Ernst Haeckel (1834-1919)
19th Century Christian
Catastrophist and anti-Darwinist
comparative anatomist who never
accepted Darwinism
important comparative anatomist
and paleontologist who identified
homologies to establish
characteristic Platonic
"archetypes," "ideal" body plans /
bauplans for higher taxa,
especially vertebrates
British naturalist, wrote On the
Origin of Species (1859) which
established that all species of life
have descended over time from
common ancestry, and proposed the
scientific theory that this branching
pattern of evolution resulted from a
process that he called natural
selection.
All true classification is genealogical
Grand analogy: Evolution is a
branching tree and organisms
change over time
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Ernst Haeckel
(1834-1919)
German
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Hans Christian
Jachim Gram
Edouard
Chatton
(1853-1938)
Danish
(1883-1947)
French
Herbert F.
Copeland
(1902-1968)
American
Robert Harding
Whittaker
(1920-1980)
American
Carl Woese
(1928-2012)
American
Only after his theory was
published did biological evolution
become an acceptable alternative
to earlier explanations
1866 – phylogenetic tree of life
Prominent biologist who
popularized Charles Darwin’s work
in Germany
Embryologist who developed
recapitulation theory (ontogeny
recapitulates phylogeny)
Three kingdom system: Plantae,
Animalia, Protista
artist (Art Forms in Nature)
Coined the term “ecology”
 1884- Developed the gram stain
method
 Defined the terms Prokaryota and
Eukaryota (1925)
 The terms had little impact on
classification for decades
 1938- proposed a four kingdom
classification, moving the two
prokaryotic groups bacteria and
“blue green algae” into the
kingdom Monera
 Copeland's Four Kingdoms:
Monera (prokaryotes), Protista
(primitive eukaryotes), Metaphyta
(plants), Metazoa (animals)
 wrote The Classification of LOWER
ORGANISMS (1956)
 American plant ecologist
 Elevated the fungi to their own
Kingdom (1969)
 proposed a five kingdom system
with Monera (prokaryotes),
Protista (primitive eukaryotes),
Mycota (fungi), Metaphyta (plants)
and Metazoa (animals)
 microbiologist who wrote The
Genetic Code (1967) that
catalogued the presence and
frequencies of various sequences
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Thomas
Cavalier-Smith
(1942present)
English
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in the 16S rRNA components of
ribosomes in representatives of
the 3 Domains
Determined that Archaebacteria
should be placed in a separate
domain-defined Archaea
proposed the three domain
classification of life with
Eubacteria, Archaea, and Eukarya
with 5-6 nested Kingdoms
Saltationist
1981- divided the domain
Eukaryota into 9 kingdoms
1993- reduced Eukaryota
kingdoms to 6
classified domains Eubacteria and
Archaebacteria
Eight kingdom system: Plantae,
Animalia, Protozoa, Fungi,
Eubacteria, Archaebacteria,
Chromista, and Archezoa
Rejects the three domain system
ENTIRELY
Chapter 8: Concepts
~Based on microfossils there is a two billion year diversification period
where cells created by abiogenesis, ~4.0-3.5 Bya, developed into the basis
for the eukaryotic cells, 2.5-2.8 Bya.
~The first successful protocells would have been heterotrophs. It is
assumed that after raw material become short on supply some of these cells
become photosynthetic autotrophs, cyanobacteria.
~Methane concentrations in ancient rocks suggest that some of the cells
produced methane as a byproduct from metabolic pathways.
~Stromatolites in the coast of Australia support the theory that life had
diversified 3.4 Bya and existed in structured, biological ecosystems.
~All organisms are bound by four essential facts1) they share a common
inheritance 2) their past has been long enough for inherited changes to
accumulate 3) the discoverable relationships among organisms are the result
of evolution 4) discoverable biological processes explain how organisms
arose and how they were modified through time by the process of evolution.
~The first two kingdoms recognized were Plantea, plants, and Animalia,
animals. This later changed to account the bacteria as another kingdom, the
Protista.
~In 1938 a proposed kingdom for bacteria and the blue-green algae was
called Kingdom Monera, all prokaryotes without nuclei or membranebound organells.
~In 1969 the fungi, classified as plants, were elevated into their own
kingdom, Kingdom Fungi.
~ Carl Woese, having performed genetic comparisons on different cell
species, was able to define three domains for the living world. The
Eubacteria, which include the bacteria and cyanobacteria, Archaea, the cells
that have cell walls made of different molecules from those found in bacteria
and cells which often live under more rigorous conditions, and the Eukarya,
which included slime molds, ciliates, and the multicellular kingdoms of the
Plantea, Animalia, and Fungi.
~Archaebacterial traits distinguishable from Eubacteria are the different cell
wall chemistry, membrane lipid chemistry, major nutrient metabolic
pathways, ribosomes and RNA polymerase and DNA associated with
histones, like Eukaryotes.
Five Kingdoms Became Three Domains
Carl Woese's Three Domains:
 Eubacteria (Bacteria) - prokaryote (lacking a nucleus or other
membrane-bound organelles) unicellular organisms with cell walls
which include peptidoglycan and may be distinguished by the Gram
stain (positive, negative, or variable); most are heterotrophic and some
are photosynthetic, a minority are chemotrophic. Most are either
coccal (spherical), rods, or spiral forms
 Archaea (Archaebacteria) - prokaryote (lacking a nucleus or other
membrane-bound organelles) unicellular organisms with cell walls
which lack peptidoglycan and are not easily distinguished by the
Gram stain; they may be heterotrophic, photosynthetic, or
chemotrophic. Some live in extreme environments. They are the
sister group to Eukarya because they use histone proteins in their
DNA supercoiling. A Domain that is sometimes also referred to as a
Kingdom.
 Eukarya (Eukaryota): DNA organized as linear chromosomes. Many
cytoplasmic membrane-bound organelles. Eukaryotic cytoskeleton and
ribosomes. Presence of external cell wall variable . Sexual reproduction
predominates, various means of gene recombination. Unicellular or multicellular.
Five Kingdoms become Six
 Thomas Cavalier-Smith (1942- ) published extensively on the
classification of protists, wrote Predation and Eukaryote Cell Origins:
A Coevolutionary Perspective (2008).
-Has been tinkering with the classification for more than a decade and
his taxa remain controversial--he rejects the three-domain system
entirely.
-Divided the domain Eukaryota into nine kingdoms. (1981)
-Reduced the total number of eukaryote kingdoms to six. (1993)
-Classified the domains Eubacteria and Archaebacteria as kingdoms,
adding up to a total of eight kingdoms of life (Plantae, Animalia,
Protozoa, Fungi, Eubacteria,
Archaebacteria, Chromista, and Archezoa)
-His classification treats the archaebacteria as part of a subkingdom
of the Kingdom
Bacteria (2004)
Cavalier-Smith's Six Kingdoms (2004):
 Bacteria
 Protozoa
 Chromista
 Plantae
 Fungi
 Animalia
~The Last Universal Common Ancestor of all organisms today had DNA as
the hereditary material, DNA replication with helicase and DNA
synthetases, ribosome-based protein synthesis, several common metabolic
pathways, ATP, phospholipid bilayer cell membrane, and active transport
across membranes.
~Cyanobacteria fossils are the oldest fossils found in Western Australia from
about 3.5 Bya making it surprising due to the fact that the earliest rocks are
only dated back to 3.8 Bya.
~Cyanobacteria dominated the globe for 2 billion years, with some forms
still existing today. They produced large quantities of oxygen by
photosynthesis which would slowly eliminate the reducing atmosphere of
early earth.
~Eukaryotic cells probably arose through endosymbiosis and incorporation
(e.g. chloroplast, mitochondria).
~Horizontal Gene Transfer, HGT, may be achieved by a virus
(transduction) or a small, circular DNA particle known as a plasmid
(conjugation) that contains a foreign gene and as much as one-third of some
prokaryotic genome has been acquired through HGT or by absorbing and
incorporating naked DNA from the environment (transformation); it may
also be achieved during endosymbiosis; it also occurs in eukaryotes by
various mechanisms.
~Less than ten-percent of eukaryotes acquired one or two protein families
through HGT.
~The three main ways of prokaryote HGT are
1) Transformation, the up-take of naked DNA from the external
environment
2) Conjugation is an HGT process by which one bacterium transfers genetic
material to another through direct contact. During conjugation, one
bacterium serves as the donor of the genetic material, and the other serves as
the recipient. They do not have to belong to the same species. The donor
bacterium carries a DNA sequence called the fertility factor, or F-factor. The
F-factor allows the donor to produce a thin, tubelike structure called a pilus
or conjugation tube, which the donor uses to contact the recipient. The pilus
or conjugation tube then draws the two bacteria together, at which time the
donor bacterium transfers genetic material to the recipient bacterium.
Typically, the genetic material is in the form of a plasmid, or a small,
circular piece of DNA of plasmid DNA, though in some circumstances, it
might be a part or all of the main bacterial "chromosome" or main circular
DNA genome. It is also the term for sexual reproduction in ciliate protistans.
3) Transduction, or transfer via viral infection.
~ prokaryotic HGT may be a beneficial process since they reproduce
asexually, but with HGT a cell can acquire a gene that confers survival or a
novel characteristic which enables them to thrive in harmful conditions or to
utilize a new metabolite. It is through this process that resistance to
antibiotics can be transferred from one bacterial cell to another.
~Another classic example for HGT is the origins of Mitochondria and
Chloroplast from endosymbiosis.
~Archaebacteria acquired organelles by endosymbiosis.
~Early Eukaryotes has cell walls, were aerobic heterotrophs, and eventually
developed sexual reproduction, which would lead to the decline of HGT
among Eukaryotic lineages likely to the alternative sexual recombination.
Chapter 9: Eukaryotic Cells and
Multicellular Organisms
Lynn Margulis
(1938- )
American
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Thomas
Cavalier-Smith
(1942-present)
English
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Sharma Barnabas
Concepts:
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Indian
Biologist who
proposed
endosymbiosis, a
hypothesis used to
explain the origin of
mitochondria and
chloroplasts
Evolutionary Biologist
who divided the
domain Eukaryota into
9 kingdoms (1981)
1993 - reduced
Eukaryota kingdoms
to 6
proposed the taxon of
Rhizaria in 2002
classified domains
Eubacteria and
Archaebacteria
Eight kingdom system:
Plantae, Animalia,
Protozoa, Fungi,
Eubacteria,
Archaebacteria,
Chromista, and
Archezoa
Rejects the three
domain system
ENTIRELY
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Along with fellow co-workers
produced a tree of life that
took into account the
nucleotide sequences from 5s
rRNA and amino sequences
(1982)
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This phylogeny provided
strong support for the
Symbiotic theory of organelle
function
Evolution of Eukaryotes
 As early as 1.5 Bya eukaryotic cells appear as fossils
 Early eukaryotes were single-celled organisms or simple filaments
 Today, most eukaryotic cells are multicellular and all contain a
nuclear membrane and organelles
 Kingdom Protista: all unicellular eukaryotes. Probably not
monophyletic
 Endosymbiotic events provided mitochondria, chloroplasts
 Microtubules drive the nuclear chromosomal division (mitosis)
Five Eukaryotic Supergroups
 Plantae (Archaeplastida): Charophyta (stem group), red algae,
green algae, and land plants
 Excavata:
o Various Protistans
o many with parasitic lifestyles
 Giardia, Trichomonas, Trypanosoma
 Chromalveolata:
o first proposed by Thomas Cavalier-Smith
o algae, heterotrophic ciliates, water molds, dinoflagellates,
diatoms
o protistan parasites
 Plasmodium falciparum
 Rhizaria: advocated for by Cavalier-Smith.
o Heterotrophic protistans
 Foraminiferans, radiolarians
 Unikonta:
o Parasitic Protistans, choanoflagellates, fungi, animals, and
Amebozoans (slime molds), amoeba
The two popular theories to explain the origin of the membrane bound
organelles
 Endosymbiosis - a well supported hypothesis which explains the
origin of chloroplasts and mitochondria and their double membranes;
This concept postulates that chloroplasts and mitochondria are the
result of many years of evolution initiated by the endocytosis of
bacteria and blue-green algae. According to this concept, blue green
algae and bacteria were phagocytized but not digested; they became
symbiotic instead and subsequently co-evolved with considerable
horizontal gene transfer between the nuclear and organelle genomes.
Other data supports an endosymbiotic origin for the eukaryotic
nucleus.
 Invagination – the plasma membrane was engulfed or invaginated to
form the endomembrane system.
Along with the theories above, were two models explaining the origin of the
Eukaryotes, the Nucleus First-Mitochondria Later Model and the
Mitochondria-Nucleus Co-origin model.
Origin of Eukaryotes
 Endosymbiosis: When ancient anaerobic eukaryotic cells engulfed
prokaryotic organisms and established a symbiotic relationship with
the prokaryote. The prokaryotes were retained as cellular organelles –
mitochondria and chloroplast – providing eukaryotes with additional
sources of DNA.
 Free-living bacteria developed mutually beneficial relationships
within a host prokaryotic cell
 Aerobic bacteria developed into mitochondria
 Cyanobacteria developed into chloroplasts
Organelle DNA differs from Nuclear DNA
 Location: organelle vs. nucleus
 Organization: singular circular vs. multiple linear strands
 Function: Which proteins coded for and how regulated
 Mode: of replication and inheritance
Mitochondrial DNA
 Single double-stranded DNA molecule
 Many mitochondria in each cell
 Similar to prokaryotic DNA because no histones or proteins, and no
introns
Chloroplast DNA
 single double-stranded circular DNA
 inherited uniparentally from the maternal (seed) parent
 1/4th of DNA of cell
Origin of Various Photosynthetic Eukaryotes
 The origin of early eukaryotic ancestors leading to the lineages of
animals and fungi was probably and independent event from that of
the origin of plants
Transfer of Genes Between Organelles and Nucleus
 Many transferred back and forth
o Ex: genes for amino acid synthesis
 Improve efficiency and reduce mutations
 Genes transferred to and from the eukaryotic nucleus are a form of
Horizontal Gene Transfer
o Complicated the establishment of phylogenies
The Molecular Clock: uses mutation rates to estimate evolutionary time of
divergence of different taxa, calibrated with fossil evidence when available.
 Mutations at a given locus add up at a constant rate in related species
o This mutation rate is the ticking of the molecular clock
o As more time passes there will be more mutations at a relatively
constant rate
o Each DNA sequence or polypeptide product will exhibit its own
"clock" speed because mutation rates vary
 Mutation rates are estimated by linking molecular data and real time
from the fossil record to calibrate the clock with the fossil record
o Higher rates are better for closely related species
o Lower rates are better for distantly related species
Organelle DNA as a Molecular Clock
 The Molecular Clock is a powerful tool for estimating the dates of
lineage-splitting events
Mitochondrial DNA and Ribosomal RNA
 Different nucleic acid molecules or gene loci have different mutation
rates
 Ribosomal RNA used to study distantly related species
o Lower mutation rates that most DNA
 Mitochondrial DNA is used to study closely related species
o 10 x faster mutation rates than nuclear DNA
o Passed down from other to offspring, so it is not subject to
recombination, making it easier to trace.
Using DNA as a Molecular Clock
 Easy to use DNA from living species to draw conclusions about
phylogeny and times of divergence
 Harder to use DNA from fossils and museums because probable
contaminated by other DNA and only have small amounts of DNA
Eukaryote Characteristics
 DNA organized as linear chromosomes
 Many cytoplasmic membrane-bound organelles
 Eukaryotic cytoskeleton and ribosomes
 Presence of external cell wall variable
 Sexual reproduction predominates, various means of gene
recombination
 Unicellular or multicellular
Eukaryotic Cell Plant
 Same basic components as the animal PLUS:
o cellulose cell wall
o central vacuole (sequesters various chemicals)
o chloroplasts that carry out photosynthesis
Eukaryotes package DNA differently
Transcription and Translation in Prokaryotes and Eukaryotes
Transcription - In the cytoplasm of prokaryotes or in the nucleus and
some organelles in eukaryotes, DNA triplets are copied into a strand of
prokaryotic mRNA codons or a strand of pre-mRNA codons, which will
become the blueprint for a structural protein to be synthesized at the
ribosomes. In eukaryotes, the pre-mRNA will undergo a series of
modifications, including excision of introns and splicing of exons, 3'
capping and addition of 5' poly-A tail, before exiting the nucleus to move
to the ribosome. Transcription also produces rRNAs, tRNAs, and
various regulatory RNAs.
 prokaryote genes lack:
o introns, no pre-mRNA processing
o No nucleus, no separation between DNA and cytoplasm
o Methods of gene regulation differ
Gene Expression
 DNA contains a sequence of nitrogenous bases which codes for the
sequence of amino acids in a protein
 Triplet code: each code is composed of 3 nitrogenous bases (A, C, G,
or U in mRNA) from genetic code
 During transcription
o 1 strand of DNA serves as a template for formation of mRNA
 Messenger RNA is processed with intron removal, before leaving the
nucleus
 (note*the bases of mRNA are complementary to the base sequence of
DNA)
 mRNA carries the codon sequence to the ribosomes (ribosomal RNA
and protein) in the cytoplasm
 Translation: mRNA codons determine the order of tRNA peptide
bond formation
 produces primary structure of protein at the ribosome
Oxidative Nutrient Metabolism
 Breakdown products of carbohydrates, fats, and proteins enter various
metabolic pathways where energy is harvested
 Oxygen is used up, Carbon dioxide is given off
Nutrient Catabolism Pathways are all interconnected
Photosynthesis
 Sunlight + 6H2O + 6CO2  C6H12O6 (nutrient sugars)+ 6O2
o autotrophic prokaryote, protistan and plant cells contain various
membrane-bound photosynthetic pigments (phycobilins,
caretenoids, and chlorophylls) which can trap light and convert
light energy to chemical energy (ATPs and NADP+s). light
energy drives one of three independent forms of atmospheric
CO2 capture (C3 carbon fixation, C4 carbon fixation, and
Crassulacean Acid Metabolism); photosynthetic eukaryotes
contain chloroplasts as the organelles of photosynthesis. The
derived chemical energy also powers the light independent
Calvin cycle which generates the glucose which may be used in
cellular respiration and starch synthesis.
Landmarks in Time
 Around 2.0 Bya: eukaryotes develop from prokaryotes by complex
means including endosymbiosis and develop sexual reproduction and
colonial life forms
 Around 1.8 Bya: O2 levels rise sufficiently that the atmosphere
becomes oxidizing
Around 1.3-0.6 Bya: multicellular (metazoan) life evolves (several times?)
Chapter 10: Plants and Fungi as
Branches of the Tree of Life
Concepts:
Important Facts:
 Land plants evolved from organisms similar to some living
green algae some ~460 Mya
 Leaves and multicellularity evolved many times
 Fungi are not simple plants but a sister group of animals
 Many of the adaptations of land plants reflect the transition
from water to land.
 Horizontal gene transfer, endosymbiosis, differentiation of
somatic and germinal tissues, and mechanisms of fertilization
were important in plant evolution.
Kingdom Viridiplantae:
o Includes land plants and green algae ( red and brown algae
excluded)
o All green plants appear to be derived from a single species of
freshwater algae.
o All green algae can be split into two major clades:
1.) Chlorophytes: exclusively aquatic
2.) Charophytes: aquatic forms which gave rise to the land
plants
General Information about plants
 Multicellularity probably began when dividing cells stopped
separating after mitosis and cytokinesis
o Advantages include increased size and opportunity for
cell differentiation and specialization
 Multicellular organisms then evolved into forms in which
most cells were somatic while a few were reproductive,
forming gametes by meiosis
 Using 18S rRNA, rbcL (ribulose-bisphosphate carboxylase
gene), and nuclear and mitochondrial genomes sequences,
investigators demonstrated that numerous lineages of
aquatic algae invaded the land
 Transformation of one of these lineages gave rise to two
major lineages:
o chlorophyte green algae
o charophyte algae and the land plants
Alternation of generations - The occurrence in one species' life history of
two or more different forms differently produced, usually an alternation of a
sexual form using meiosis to generate recombinant gametes with an asexual
form using mitosis to generate identical clonal offspring in the life cycle of a
multicellular plant or animal. In land plants, the asexual form/tissue is
composed of haploid cells and the sexual form/tissue is composed of diploid
cells. In the earliest evolved land plants (bryophytes), the haploid
sporophyte tissue was dominant, i.e., it was the tissue of the individual that
persisted throughout life while the diploid reproductive tissue formed a
temporary additional structure during periods of sexual reproduction which
were often times of environmental stress. In the later derived land plants,
primarily the ferns, gymnosperms, and angiosperms, the diploid sporophyte
tissue is dominant, and the gametophyte tissue is reduced to small numbers
of temporary cells that exist only during the time for fertilization, e.g.,
ovules and polar bodies in females, and pollen grains and pollen tubes in
males.
The four major plant groups are
1.) Seedless non-vascular plants- these are plants with no seeds or
veins. These are the simplest plants; they have limited distribution
and are restricted to wet areas, and collectively known as
bryophytes (liverworts, club mosses, and hornworts). They the
first fossil evidence is of them appeared to date back to 420Mya in
the Devonian period, and then later in the Carboniferous 350Mya
ago. They major importance of bryophytes is that they represent
the beginning transition from water and the dominance of a
diploid sporophyte life cycle.
a. Bryophytes:
i. The “simplest” land plants, limited to moist
environments, are bryophytes
ii. Liverworts at 420 Mya;
iii. Mosses at 350 Mya
iv. Bryophytes were important in two major transitions:
1. water to land;
2. haploid gametophyte-dominated life cycle to a
diploid sporophyte-dominated life cycle.
Vascular seedless plants- the evolution of the cambium permitted plants to
increase in size. The cambium is the tissue from which new cells are
produced to increase the diameter of plant stems. This allows plants to grow
taller allowing them to receive more light and nutrients through xylem and
phloem tubes. These plants reproduce by using spores which need to be
spread by the environment. One of the most common plants in this group is
ferns. Ferns are also the first vascular plants with true leaves.
1.) Gymnosperms- are plants which contain cones or alternatives to
seeds contained in true fruits. These are plants such as ginkgo,
cycads, and cypress trees.
a. Gymnosperms are plants with “naked seeds”
i. Ovule is exposed on a scale at pollination
b. There are four living groups
i. Coniferophytes
ii. Cycadophytes
iii. Gnetophytes
iv. Ginkgophytes
c. All lack the flowers and fruits of angiosperms
d. Probably descended from progymnosperms
i. Seeds had evolved by end
of Devonian period
ii. Adaptive radiation in
Carboniferous and early
Permian produced the
gymnosperm divisions
iii. Largely replaced seedless
vascular plants
iv. Better adapted to drier
(Pangean) climate
2.) Angiosperms- these are flowering plants and also closely tied to
dicots, which have two seed leaves. These plants have elaborate
flowers which are used as reproductive organs which can be
specific to certain animal pollinators or open to any pollination
method.
a. Their origin is a mystery
b. Evolution and elaboration of flowers as reproductive organs
c. Evolution of diverse flower structures that enable insects,
birds, and less often other animals to pollinate them
d. Evolution of diverse seed forms and mechanisms of
dispersal
e. Life Cycle
i. The double fertilization in Angiosperms to produce
the nutritive triploid (3N) endosperm is the pinnacle
of advanced parental care in plants
ii. It is comparable to the cleidoic egg of reptiles, birds,
and montremes, and then the intrapouch and
intrauterine development of embryos seen in the
marsupial mammals
iii.
1. Mitotic division produces embryo
a. Rudimentary root
b. One (monocots) or two (dicots) seed
leaves
iv.
1. Mitotic division produces energy-rich
endosperm
2. Ovule matures into a seed
v. Why double fertilization?
1. Synchronizes development of food storage
with seed development
2. Without fertilization,
neither will occur
3. Resources are not wasted
on infertile ovules
Origin of leaves- the origin of leaves has two good hypotheses:
1.) The telome hypothesis which says leaves arose from webs between
flattened branches.
2.) The enation hypothesis which says leaves arose from small flaps or
extensions of tissue along the stem.
*We know that leaves evolved multiple times therefore, either of the two
modes for the origination of leaves can explain how the may have
developed between different lineages.
Transitions for plants:
 Origin of the land plants (embryophytes)
o Land Plant Phylogeny
o
 Origin of the vascular plants (tracheophytes)
o Early Vascular Plants
 “Vascular” refers to the presence of conductive tissue:
 xylem that enables water to reach the erect parts of
the plant;
 phloem that enables nutrients to be distributed
from the leaves and stems.
 Cooksonia, the first vascular land plant, appeared about
420 Mya
 -Only a few centimeters tall

-No roots or leaves

-Homosporous
 Origin of the seed plants (spermatophytes)
 Origin of the flowering plants (angiosperms)
Plant Life Cycles
As more complex land plants evolved:
1.) The spores became unequal in size
2.) The diploid stage became the dominant portion of the life cycle
3.) The gametophyte became more limited in size
4.) The sporophyte became nutritionally independent
These changes, along with improvements in morphology allowed radiations
into drier habitats
Moving onto Land
 Three evolutionary changes:
o reduction in the size of the gametophyte
o evolution of easily dispersible pollen
o and encasement of spores in seeds
 Allowed plants to avoid desiccation and so move away from water
Flower pollination mechanisms:
 In order for a flower to be pollinated, pollen must be moved from the
anthers to the stigma of the same or different flowers
 Whatever moves or carries the pollen is called a vector.
 There are five different classes of vectors:
o wind / water / insects /
mammals / birds
 Flowers and the animals which pollinate them have often evolved
very close relationships in which both are totally reliant on each other
 The plant for reproduction, the vector for some aspect of it biology,
often nutrition
Angiosperms- evolution and elaboration of flowers as reproductive
organs, evolution of diverse flower structures to allow insects, birds and
other organisms to pollinate them, also evolution of diverse seed forms
Sperm plus egg equals diploid zygote
1. Mitotic division produces embryo
Sperm plus nuclei equals 3n nucleus
1. Mitotic division produces energy rich endosperm
2. Ovule matures into a seed
Double Fertilization
1. Why? Synchronizes development of food storage with seed
development
2. Without fertilization neither will occur
Angiosperm radiation1. Radiation of angiosperms marks the transition from the Mesozoic
era to the Cenozoic era
2. Adaptive radiation made angiosperms the dominant plants on earth
by the end of the cretaceous
Convergent Evolution Produces Ecological Equivalents
1. Cacti from all different places
Coevolution1. Plant-pollinator coevolution is responsible for the diversity of
flowers
2. The pollinator gains nectar, and pollen and the plant gains cross
pollination
Coevolution- Plants have influenced the evolution of animals and vice
versa
Darwin and coevolution1. Darwin hypothesized that a hawk moth with a long proboscis would exist to pollinate the
Madagascar star orchid, a century later such a hawk moth was found
Fungi1. First appeared along with the first vascular plants in the Silurian
Fungi- are not simple plants, share an ancestor with animals, are more
closely related to animals than plants
Characteristics1. Eukaryotic, non-photosynthetic, some are parasitic, uni or
multicellular, avascular
2. Have an alternation of generations life cycle, reproduction by
spores or asexually, non-motile usually, decomposers and
recyclers of nutrients in environment
3. Absorptive heterotrophs, release digestive enzymes to break
down organic materials or their hosts, store food energy as
glycogen, build complex carbohydrate cell walls
4. Some are internal or external parasites, a few of them act like
predators and capture prey like roundworms
5. Some are edible and some are poisonous
6. Produce both sexual and asexual spores, classified by the sexual
reproductive structures, some have no sexual phase
7. Penicillin is made by the penicillium mold
Reproductive structures1. Basidia, sporangia, and asci
2. Spores consist of- haploid cell, dehydrated cytoplasm, protective
coat
3. Spores germinate when they land on a moist surface
Classification by nutrition1. Saprobes are decomposers and mold or mushrooms
2. Parasites- harm host, rusts and smuts
3. Mutualisms- both benefit, lichens and mycorrhizas
Major groups of fungi
1. Basidimycota- club fungi
2. Zygomycota- bread molds
3. Chytridiomycota- chytrids
4. AM fungi- arbuscular mycorrhyizas
5. Ascomycota- sac fungi
6. Lichens- symbiosis
Lichens- mutualism between fungus (often a yeast and an ascomycete),
algae or cyanobacteria and they form a thallus or body; they can inhabit
more extreme environment by trading water and minerals from the fungus for
photosynthetic carbohydrates from the algae; the fungi usually cannot live
independently of the algae, its photosynthetic partner, but the algae or
cyahobacteria can live independently of its fungal partners.
Chapter 11: Animals as a Branch
of the Tree of Life
William Smith
(1769-1839)
English

Sir Richard
Owen
(1804-1892)
British





Sir D’Arcy
Wentworth
Thompson
(1860-1948)
Scottish


Proposed the geological Principle
of faunal succession: noted that
different rock strata contain
particular types of fossilized flora
and fauna, and that these fossil
forms and communities succeed
each other in a specific and
predictable order that can be
identified over wide distances
19th Century Christian
Catastrophist and anti-Darwinist
comparative anatomist who never
accepted Darwinism
important comparative anatomist
and paleontologist who identified
homologies to establish
characteristic Platonic
"archetypes," "ideal" body plans /
bauplans for higher taxa,
especially vertebrates
Archetype and Homologies of the
Vertebrate Skeleton (1848)
On the Nature of Limbs (1849
an early attempt to argue for
constraints on organismal design
from purely physical, mechanical,
chemical principles
biologist, mathematician and
classics scholar who argued for
constraints on organismal design
the central theme of On Growth
and Form (1917) is that biologists
of the early 20th century
overemphasized evolution as the
fundamental determinant of the


David Raup
(1933-2015)
American




William Bateson
(1861-1926)
British

form and structure of living
organisms, and underemphasized
the roles of physical laws and
mechanics.
advocated for structuralism as an
alternative to the “survival of the
fittest”/Darwinism in governing
the form of species
explored the degree to which
differences in the forms of related
animals could be described by
means of relatively simple
mathematical transformations, a
major early contributor to the
concept of allometry, the study of
biological scaling
Paleontologist and paleobiologist
who developed a more
mathematical modern hypothesis
of the bauplan, the morphospace
developed a method to plot the
morphologies of organisms in the
N-dimensions in what he termed
morphospace, which he
represented a cube or higher
dimensional space with different
features of organisms along each
axis.
Raup’s analysis showed that the
known morphologies of shelled
invertebrates cluster in one region
of the morphospace, a cluster that
demarks the limits of the body
plan in these organisms and that
not all forms were found in nature.
Raup concluded that unoccupied
morphospace represented
impossible morphologies,
nonadaptive morphologies and/or
constraints on morphology
studied the cyclic nature of major
extinction events in the past
First recognized and coined the
term homeotic mutations in

Francois Jacob
(1920-2013)
French


Adolf (Dolf) Seilacher
(1925-2014)
German

Guy Narbonne
(?- )
Canadian


Joseph L. Kirschvink
(?- )
American

Materials for the Study of Variation
(1894)
He was the first person to use the
term genetics to describe the
study of heredity and biological
inheritance, and the chief
populariser of the ideas of Gregor
Mendel following their
rediscovery in 1900 by Hugo de
Vries and Carl Correns
A founder of molecular biology
and Nobel prize winner associated
with the Lac Operon
Referred to evolution as bricolage
(tinkering)
paleontologist who placed Ediacaran
organisms into a distinctive group, the
Vendozoa, which he and others regard as
unrelated to any animals; a separate
evolutionary experiment.
paleontologist who invoked repeated structure
based on fractal repeats of a frond structure in
his analyses of early Ediacaran organisms to
identify a major group which he named
rangemorphs
Narbonne is cautious when it comes to saying
whether rangemorphs were animals or an
alternative and earlier evolutionary experiment
in multicellularity
1989 - originator of the snowball (or
slushball) earth concept; a self-reversing
climate instability driven by ice-albedo
feedback and massive volcanism that put
massive amounts of dust in the atmosphere
Concepts
 The entire earth was encased in a sheet of ice 1 km thick two to four
times between 725 and 635 Mya. (Snowball Earth)
 Communities of enigmatic organisms -- the Ediacaran / Vendozoan
Biota -- existed in the Upper Precambrian more than 565 Bya,
before animals appear in the fossil record.
o Formed complex ecosystems.
o Disappeared early in the Cambrian.
 Based on molecular evidence we can conclude that animals originated
in the Precambrian 700-750 Mya.
 Animals of all major phyla first appear as fossils 545 Mya in the Early
Cambrian Burgess Shale and equivalent faunas worldwide.
 Stem taxa of animal phyla therefore must be Precambrian in age.
 Reasons for the origination of animals include the elaboration of
genes and embryonic development, environmental and climate
changes in the level of atmospheric oxygen.

Bauplan concept: placed more emphasis on the physical and
chemical restraints on organisms and how that forced them to evolve a
certain way
 Morphospace: The totality of possible body shapes that a species
or other taxon can assume as it evolves, or that an organism can
take as it develops, as defined by genetic, ecological, or other
factors.

Types of temporal bone openings:
o Anapsid- ancestral form with holes only for the eyes and
nostrils( turtles)
o Synapsid- form that has one other hole besides the ones for the
eyes and nostrils (mammals)
o Diapsid- form that has 2 other holes besides the ones for the
eyes and nostrils (crocodilians, birds and dinosaurs)
 Homeobox genes that pattern animal bodies originated before
animals, plants, and fungi arose. They encode for transcription
factors.
 About 5545 Mya in the Early Cambrian, an explosive radiation of
multicellular organisms with soft and hard tissue appears in the fossil
record.
 Multicellularity facilitated cellular specialization within organisms
and structural differences between organisms, the evolution of
different modes of food gathering, and enormous increase in body
size.
 Some explanations to how animals radiated and diversified so
quickly:
o A rise in atmospheric oxygen
o Changing geological features
o Recovery from snowball earth
o Origination or elaboration of embryonic development
o Diversification of mechanisms of gene regulation
o The evolution of predator-prey interactions associated with the
opening up of new ecological zones
 Animal origins:
o choanoflagellates are ~150 living species (no fossils) of singlecelled and colonial protistans (the collared flagellate cell
morphology is similar to the choanocytes (collared cells) of
sponges and ribbon worms); they are motile predators who
were either animal ancestors or choanoflagellates and animals
descended from a common protistan ancestor; their
synapomorphies include certain cell adhesion molecules.
o The absence of features usually associated with prey capture,
and the absence of digestive tracts, led to proposals that many
Ediacaran / Vendozoan organisms may have depended on
photosynthetic or other types of symbiosis with
microorganisms.
o The organisms in the Ediacaran / Vendozoan Biota did not have
larval forms, eyes, mouths, anuses, intestinal tracts, or
locomotory appendages.
 Characteristics of animals:
o Eukaryotic, never photosynthetic
o Multicellular, usually with differentiation into tissues; avascular
and vascular forms
o Life cycle lacks alternation of generations
o No cell walls
o Sexual and asexual reproduction by often complex structures
and life cycles
o Enhanced responsiveness and motility due to nervous,
endocrine, and musculoskeletal systems
 Animals arise:
o By the beginning of the Cambrian 545 Mya, many different
types of animals were present, recognizable, and can be
classified on the basis of their different body forms.
o Burgess Shale Fauna:
 A 545 My old limestone reef assemblage of superbly
preserved fossils located in British Columbia, Canada at
160 m deeps and more than 20 km long and which
records the Cambrian Explosion of animal body forms.
Includes arthropods, sponges, brachiopods, polychaete
worms, echinoderms, cnidarians, and mollusks.
o 3 important conclusions to assign organisms from Burgess
Shale to clades:
 These organisms are crown taxa that already had evolved
the characters that define the phyla of living animals.
 Morphological gaps separated these crown taxa.
 Origination of phyla from stem taxa has to be sought in
earlier form in older deposits.
 The only evidence we have to recognize and classify Early Cambrian
organisms is morphological.
o One class of morphological evidence comes from the
preservation of cleavage-stage animal embryos in Late
Precambrian and Early Cambrian rocks.
 While not numerous, these specimens have given us a
glimpse of jellyfish development 530 Mya, and of the
presence of segments in early embryos.
 The absence of any fossilized larval stage strongly
suggests that early animals developed directly without a
larval stage (direct development).
 A Cambrian “Explosion”
o The diversity of Cambrian organisms could be interpreted as
adaptive radiation in which many new ecological opportunities
were made available for organisms with the capacity to evolve
in diverse ways so as to occupy and exploit the changing
environments.
o Divergence among major Cambrian lineages began in the
Precambrian about 700 Mya.
o Modifications during the Cambrian added hard parts and
mineralized skeletons that provided leverage for evolving
muscles, support for body organs, enclosures for gills and
filtering systems, and protective shells and spines.
 Causes of the Cambrian Radiation:
o Geological, environmental and climatic conditions
o Changing oxygen levels
o Predator-prey relationships
o Evolution of embryonic development and body plan
specification
o New sources of genetic variation and changes in gene number
and regulation
 Geological conditions:
o Animal fossils may be absent from Precambrian rocks because
geological conditions prevented fossilization or destroyed and
fossils present; the heat and pressure involved in Precambrian
mountain building has been proposed as an important factor
limiting fossilization.
 However, prokaryotic and eukaryotic organisms were
preserved in the Precambrian so it is unlikely that the
Cambrian discontinuity is unreal and merely the
consequence of geological metamorphism or imperfect
fossilization.
o Plate tectonics and sea level changes would also have played a
role in new environments.
 Rising Oxygen Levels
o Oxygen forms a protective blanket of ozone that could have
facilitated the expansion and radiation of multicellular animals
in shallow waters, tide pools, and nearby rocky surfaces.
o Aerobic metabolism, which is dependent on oxygen,
facilitated the use of new sources of energy, permitting increase
in body size.
o Animals capable of exploiting Early Cambrian oxygen would
have possessed a battery of common genes including those for
hemoglobin, which is a conveyer of molecular oxygen.
 Predator-prey relationships
o There was a change in the modes of feeding facilitated by rising
oxygen levels.
o Predators feed on the most abundant prey species, reduce the
numbers of prey, and so allow other species to use resources
formerly monopolized by the dominant prey.
Crucial Vertebrate Transitions:
o origin of jaws
o origin of fins and later limbs for locomotion/origin of the lungs
o origin of the cleidoic egg
o origin of the advanced water conserving vertebrate kidney
o two separate origins of endothermy and associated insulation
o origin of pouch or placenta for embryo support and protection
 Shared Embryonic Development and Body Plan Specification
o Most distinctive morphological features of almost all adult
animals:
 Axes of symmetry, usually anterior-posterior (A-P),
dorso-ventral (D-V), and left and right (L-R).
 Paired appendages
 Similar tissues and organs
 Homeobox genes
o Contain the homeobox
o Each homeobox gene codes for a polypeptide sequence about
60 amino acids long called a homeodomain.
 Major conclusions from studies of comparative gene structure and
function:
o These important developmental (regulatory) genes all share a
common, highly conserved, and evolutionary ancient role as
transcription factors.
o A common genetic evolutionary origin underlies the
conservation of the basic developmental pathways that establish
animal body plans.
o What has changed with evolution is context; the specific
function of these conserved regulators varies from cell lineage
to cell lineage, tissue to tissue, organ to organ, as well as from
time to time during development.
 Mammalian Shared Derived Characters
o Endothermy with insulating hair and subcutaneous fat
o Mammary glands; extended parental care
o Uterus and colon (no cloaca)
o Dentary-squamosal jaw joint
o 3 ear ossicles
o Expanded cerebral cortex
o Heterodonty and buccal cavity (cheeks)
Vocabulary:
1)
Ediacaran Fauna / Ediacaran Biota- multicellular organisms
that remain enigmatic.
2) Archaeopteryx- the 'missing link' that shows a transitional stage
between birds and dinosaurs
3) Heterodonty- applies to animals that possess more than one type of
tooth morphology
4) Ichthyosaur- giant marine reptile that lived during the Mesozoic era.
Developed from land reptile that made the transition back into the
water.
5) Biota- a more appropriate term for the organisms found in a region or
a geographical period.
6) Fauna- refers to the animal life found in a region or a particular time.
7) Stem taxa-the earliest representation of a lineage. There can only be
one stem taxon for a lineage.
8) Crown taxa- the terminal branches of a lineage arising from a stem
taxon. A single lineage may have more than one crown taxon.
9) Vendozoa- a distinctive group of Ediacaran organisms that are
regarded as unrelated to any animals.
10)Modularity-concept that units of life, such as gene networks,
aggregations of cells and organ primordial, develop and evolve as
units (modules) that interact with other modules.
Allometry- also called biological scaling, in biology, the
change in organisms in relation to proportional changes in body
size. An example of allometry can be seen in mammals. Ranging
from the mouse to the elephant, as the body gets larger, in general
hearts beat more slowly, brains get bigger, bones get
proportionally shorter and thinner, and life spans lengthen. Even
ecologically flexible characteristics, such as population density
and the size of home ranges, scale in a predictive way with body
size. The study of allometry stems from work in the late 19th
century by the Scottish zoologist D’arcy Thompson and in the
early 20th century by the English biologist Julian Huxley, the
latter of whom coined the term for this field of study. On the
concept of allometry, D’arcy Thompson wrote: "An organism is so
complex a thing, and growth so complex a phenomenon, that for
growth to be so uniform and constant in all the parts as to keep the
whole shape unchanged would indeed be an unlikely and an unusual
circumstance. Rates vary, proportions change, and the whole
configuration alters accordingly."
11)
12)Fractal-a shape that can be split into parts each of which has the same shape as the original (a fern
leaf).
13)Rangemorphs-existed in complex ecological communities with more than one trophic level with
frond-like organization 570-575 Mya.
14)Monoblastic animals - show the simplest metazoan organization,
having a single germ layer such as sponges. Although they have
differentiated cells, they lack true tissue organization.
15)Diploblastic animals - members of the phyla cnidaria and ctenophora
show an increase in complexity, having two germ layers, the
endoderm and the ectoderm organized into recognizable tissues.
The embryonic ectoderm develops into the epidermis, nervous system,
and, if present, nephridia; the embryonic endoderm develops into the
gut and associated glands.
16)Triploblastic animals - possess a mesoderm as well as the endoderm
and ectoderm. They are the remaining animal/metazoan phyla from
flatworms to birds and mammals, most of which show bilateral
symmetry. They show radial or spiral cleavage and develop
recognizable organs. The embryonic ectoderm develops into the
epidermis and its derivatives, nervous system; the embryonic
endoderm develops into the gastrointestinal, respiratory and urinary
tract and their associated glands, the secretory cells of the endocrine
glands, and the auditory system; the embryonic mesoderm develops
into body cavity linings, if present, mesenteries, parts of the
reproductive system, musculo-skeletal systems, blood vessels and
blood cells, the kidneys, the adrenal cortex, and the dermis and other
connective tissues.
17)The plankton explosion-a marked increase in size, diversity, ornamentation and turnover rate
among eukaryotic plankton (acanthomorphic acritarchs), which is tentatively attributed to
predation by eumetazoa.
18)Morphospace-3-D representation of the morphological characters of
an organisms or group of organisms used to show how much of the
possible range of morphologies is expressed.
19)Protostomes - a feature of the blauplan in the majority of triploblastic
coelomate invertebrate metazoans other than echinoderms, most of
whom show bilateral symmetry, a clade of organisms whose
embryonic blastopore becomes the mouth of the adult.
20)Deuterostomes – a feature of the blauplan in the majority of
triploblastic coelomate metazoans, the echinoderms, chaetognaths,
hemichordates, and chordates, most of whom show bilateral
symmetry, a clade of organisms whose embryonic blastopore becomes
the anus of the adult.
21)Acoelomates-no true body cavity (flatworms)
22)Pseudocoelomates - triploblastic metazoan animals which possess a
"false" body cavity, in which a fluid-filled cavity is only partially
bounded by mesodermal tissue; lacking any mesenteries to support
internal organs; and no muscular layers around the gut tube to provide
peristalsis; examples include round worms and some other protostome
invertebrates.
23)Coelomates - triploblastic metazoan animals which possess a true
body cavity lined with a mesodermal lining; having internal organs
suspended in mesenteries; and muscular layers around the gut tube to
provide peristalsis during digestion; examples include most bilaterally
symmetrical animals, most invertebrates and the chordates
24)Cephalization-an evolutionary trend in which nervous tissue becomes
concentrated toward one end of an organism, eventually producing a
head region with sensory organs.
25)Co-evolving arms race-successive rounds of selection for predator
responses to their prey’s protective devices, followed in turn by
adaptations by the prey to their predator’s devices, promoting
diversity.
26)Homeobox genes - any of the evolutionarily conserved genes which
are translated into embryonic regulatory (homeo)proteins that act as
DNA binding transcription factors that provide the primary signals
and initiate the pathways in animals that help differentiate bands and
clusters of cells that organize the pattern (anterior/posterior,
dorsal/ventral, right/left) of body regions and the formation of
particular structures such as internal organs, and body extensions,
sense organs, antennae, wings and legs, etc. They exist and play
similar roles in the development of higher plants and fungi. A
homeobox gene codes for a polypeptide sequence about 60 amino
acids long called a homeodomain. These important
developmental (regulatory) genes all share a common, highly
conserved, and evolutionary ancient role as transcription factors.
A common genetic evolutionary origin underlies the conservation
of the basic developmental pathways that establish animal body
plans. What has changed with evolution is context; the specific
function of these conserved regulators varies from cell lineage to
cell lineage, tissue to tissue, organ to organ, as well as from time to
time during development. Axes of symmetry, usually anteriorposterior (A-P), dorso-ventral (D-V), and left and right (L-R).
Their sequential arrangement on the chromosome usually
matches their developmental action cranial to caudal in the
embryo.
27)Morphogens- activate pathways leading to the development of an
organism’s form or part of an organism.
28)Antennapedia complex-cluster of six Antennapedia-linked genes
first discovered in fruit flies whose activation converts anterior into
posterior body structures.
29)Homeotic mutations (homeosis)-In modern genetic usage, homeotic
mutations cause the development of tissue in an inappropriate
position; for example, bithorax mutations in Drosophila produce an
extra set of wings.
30)Bricolage-(tinkering) a term that rightly places the emphasis on modification of existing genes.
31)Homeodomain- part of a transcription factor that binds to DNA, there
by regulating mRNA production.
32)Hox gene family-homeobox gene in vertebrates, taking the gene
name from the first two letters of the orthologous gene in Drosophila
and adding an x. Show colinerarity, control organogenesis, are
homologous among Metazoans. Example of a hox gene mutation extra ribs.
33)Gene regulation- has emerged as a central mechanism explaining
developmental and evolutionary change.
34)Paralogous genes (paralogues)-two or more different loci in the same organism that are
sufficiently similar in their nucleotide sequences (or in the amino acid sequences of their protein
products) to indicate they originated from one or more duplications of a common ancestral gene.
35)Orthologous genes (orthologues)- gene loci in different species that are sufficiently similar in
their nucleotide sequences (or amino acid sequences of their protein products) to suggest they
originated from a common ancestral gene.
36)Gene family- two or more gene loci in an organism whose similarities
in nucleotide sequences indicate they have been derived by
duplication from a common ancestral gene.
37)Ostracoderms- the earliest vertebrates (shell-skinned) are groups of
extinct, primitive, jawless fishes that were covered in an armor of
plates of true bone tissue. Small, slow swimming, bottom-dwellers.
Likely the first animals to use their gills for respiration.
38)Orthogenesis- progressive pattern of improvement of a species
without much branching (example: the teeth of horses)
39)cleidoic egg- the type of egg laid by reptiles and birds; it allows them
to reproduce out of and away from water by providing a moist
environment for the embryo
Chapter12: Individual Genetic
Variation and Gene Regulation
Edward B.
Lewis
(1918-2004)
American





Barbara
McClintock
(1902-1992)
American


founder of developmental
genetics
studied the bithorax and
related mutants in Drosophila
and their controlling homeotic
genes in DNA in the 1970s
through 1990’s
this led to the new
subdiscipline ”Evo-Devo”
[evolutionary development]
he laid the groundwork for our
current understanding of the
universal, evolutionarily
conserved strategies
controlling animal
development.
1995- Nobel Prize in Medicine
for discoveries concerning the
genetic control of early
embryonic development
1944-1953 discovered
transposons and gene
regulation in maize though her
work was ignored and
misunderstood for decades
1983- Nobel Prize for
Medicine/Physiology for her
discovery of Genetic
Transposition.
Ernst Mayr
(1904-2005)
German/American





Francois Jacob
and Jacques
Monod
FJ (19202013) & JM
(1910-1976)
French

Andre Lwoff
(1902-1994)
French

Regarded as the greatest
evolutionary biologist of the
20th century
Defined the Biological Species
Concept in 1942
His last version of the BSC
(2001) states: "Species are
groups of interbreeding natural
populations that are
reproductively isolated from
other such groups."
A founder of the Modern
Synthesis
His last book, “What Evolution
Is”, published 2001, is a
thorough and thoughtful
exploration of Evolutionary
Biology
In 1961 on the genes governing
the production of enzymes
involved in lactose sugar
metabolism in the bacterium E.
coli. This is the first study
leading to the discovery of gene
regulation. For this
fundamental discovery, they
received the 1965 Nobel Prize
in Physiology and Medicine.
The director of the Pasteur Institute
where Jacob and Monod conducted their
experiments, received the 1965 Nobel
alongside of Jacob and Monod.
Concepts
 Regulatory mutation: changes that generally affect genes controlling
genetic pathways or networks
 Natural selection acts on existing phenotypic variation
 Mutations are necessary for evolution
o Spontaneous mutations











o Induced mutations
o Somatic mutations
o Germline mutations
Point mutations occur through substitutions, insertions, deletions,
transposition
Substitution mutation - A type of point mutation in which a single
nucleotide is substituted with (or exchanged for) a different nucleotide
that may result in an altered sequence of amino acids during
translation, which may change the protein function/phenotype or
render the newly synthesized protein ineffective.
Insertion mutation - A type of point mutation resulting from the
addition of one or more nucleotides in a DNA sequence or
chromosome.
A deletion mutation- when part of a DNA molecule is not copied or
breaks away and is lost during DNA replication. This uncopied part
can be as small as a single nucleotide or as much as an entire
chromosome. The loss of this DNA during replication can lead to a
change in protein structure and phenotype and in some cases to a
genetic disease.
Point mutations can be silent (more likely when it occurs in the third
position of the codon triplet), replacement, or stop codon
o Sickle Cell is an example of a point mutation; it results from a
mutated allele of the hemoglobin beta chain.
A mutation will only be passed to offspring if the mutation occurs in
the germ cells leading to gamete production
Somatic mutation: mutation acquired in any other cell – will not be a
heritable mutation
Most chance mutations are likely to disrupt and not improve protein
function if there is any effect at all
Sense mutation: change in DNA base, no change in amino acids
Missense mutation: change in DNA base and change in amino acid,
but protein still functional
Nonsense mutation: change in DNA base and change in amino acid,
and the protein is non-functional, a fragment, or not produced at all
 Pleiotropic effects – multiple effects
o A mutation can have a wide variety of effects if the individuals
with the mutant allele are exposed to a wide variety of
environmental conditions or selection pressures.
 Transposons or “jumping genes” direct the synthesis of additional
copies of themselves in the host genome
 Transposons may cause frameshift or other mutations.
 Chromosome number variation
o Entire sets of chromosomes
o Single chromosomes within a set
 Polyploidy = repetitive doubling
o More than 2 homologous sets of chromosomes
o Commonly found in plants
o May occur due to abnormal cell division with nondisjunction
o Especially common among ferns and flowering plants
 Plants may become tetraploid due to self-fertilization as well as less
commonly in animals by parthenogenesis (reproduction by females
without fertilization by males
 Plants may be able to survive better being polyploidy than animals
because they can tolerate extremely divergent structural relationships,
unlike animals
 Changes in the appearance (phenotype) of a chromosome (usually
observed in karyotype analysis):
o Deletions & deficiencies: remove chromosomal material
o Duplications: improperly repaired chromosome breakage
moves genes (DNA fragments) from one homologous
chromosome (which now has a deletion) to the other
homologous chromosome (which now has a duplication). Gene
duplications are the source of most new genes (loci) as well as
the development of families of related genes, such as the globin
chain families.
o Inversions: reversals in chromosome gene order
o Translocation: improperly repaired chromosome breakage
moves genes from one homologous chromosome to another
nonhomologous chromosome, the resulting hybrid segregating
together at meiosis; balanced translocations (in which there is
no net loss or gain of chromosome material) are usually not
associated with phenotypic abnormalities, although gene
disruptions at the breakpoints of the translocation can, in some
cases, cause adverse effects, including some known genetic
disorders; unbalanced translocations (in which there is loss or
gain of chromosome material) nearly always yield an abnormal
phenotype. In the simplest cases of translocation, a single locus
would move; in the largest case, an entire chromosome might
be added to a nonhomolog.






o
Inversion loops protect linked alleles from being separated by
crossing over. When alleles on two homologous chromosomes have
been rearranged so that one DNA molecule has the reverse sequence
of loci from the other, the during synapsis of Meiosis I Prophase and
Metaphase, the DNA molecules will form an inversion loop.
o Alleles in the inverted region are protected and passed as unit to
future generations
microRNAs (miRNA) regulate translation of mRNA into protein in
plants and animals
When a diploid gamete fertilizes a normal haploid gamete a triploid
individual is produced. These sets of 3 like chromosomes have
difficulty in the close alignment of synapsis
Equal crossing over provides new arrangements of alleles but has little
potential for new variation
Unequal crossing over causes duplications on one chromosome and
deletions on the other. The duplications allow for new possibilities
for gene function in eukaryotic evolution.
Mutations are expressed in gene activity:
o Changes within a gene product
o Changes in the regulation of a gene or its product
o May affect rate at which a gene is produced or whether or not
the protein is produced
 Phenotypic variation: anatomy, biochemistry, physiology, behavior,
etc.
 Genotypic variation: alleles, loci, chromosomes, genomes
 Mutation events increase genetic variation in populations and give
natural selection material from which to generate adaptive
evolutionary changes
 Most mutational processes are harmful and lead to decreased
adaptation most of the time
o But individuals being so numerous and given many millions
and billions of years to work with, beneficial changes do occur
 3 Major regulatory mechanisms control transcription of DNA
o ciso transo RNAi-regulation
 Minor mechanisms:
o Transposons
o Posttranscriptional modification
 Cis-Regulation elements
o Elements reside upstream from promoter region on same
chromosome
o Transcription factors – bind to cis-regulatory elements to
encourage or discourage transcription
 Trans-regulation
o DNA sequences that encode transcription factors
o Reside on other DNA molecule than the regulated gene
o TF’s can bind to cis-reg. elements or CAAT and TATA boxes
adjacent to a structural gene.
 Posttranscriptional modifications of eukaryotic nuclear (not organelle)
mRNA
o Introns must be removed from the transcribed pre-mRNA base
sequence and there can be options as to which introns are
removed and which exons are spliced to form the functional
mRNA
o Addition of the 5' (7-methylguanylate nucleotide) cap reduces
degradation of the capped mRNA by 5' exonucleases; facilitates
exit to the cytoplasm through the nuclear pore and assists in
orienting the capped end of the mRNA to the ribosome to
initiate translation
o Addition of poly-A tails of various lengths affects the lifespan
of the mRNA in the cytoplasm before it is degraded and
therefore, how many polypeptide chains can be translated from
one mRNA
o Other modifiers (proteins and regulatory RNAs) can bind to the
mRNA to delay or prevent translation.
 Small interfering RNA (siRNA), sometimes known as short
interfering RNA or silencing RNA, is a class of double-stranded RNA
molecules, 20-25 base pairs in length. siRNA plays many roles, but it
is most notable in the RNA interference (RNAi) pathway, where it
interferes with the expression of specific genes with complementary
nucleotide sequences. siRNA functions by causing mRNA to be
broken down after transcription,[1] resulting in no translation. siRNA
also acts in RNAi-related pathways, e.g., as an antiviral mechanism or
in shaping the chromatin structure of a genome.
 microRNA (miRNA) - small non-coding RNA molecules
(containing about 22 nucleotides) found in plants, animals, and some
viruses, which functions in RNA silencing and post-transcriptional
regulation of gene expression. Encoded by eukaryotic nuclear DNA
in plants and animals and by viral DNA in certain DNA viruses,
miRNAs function via base-pairing with complementary sequences
within messenger mRNA molecules. As a result, these mRNA
molecules are silenced by one or more of the following processes: 1)
cleavage of the mRNA strand into two pieces, 2) destabilization of the
mRNA through shortening of its poly(A) tail, and 3) less efficient
translation of the mRNA into proteins by ribosomes. miRNAs
resemble the small interfering RNAs (siRNAs) of the RNA
interference (RNAi) pathway, except miRNAs derive from regions of
RNA transcripts that fold back on themselves to form short hairpins,
whereas siRNAs derive from longer regions of double-stranded RNA.
The human genome may encode over 1000 miRNAs, which are
abundant in many mammalian cell types and appear to target about
60% of the genes of humans and other mammals. miRNAs are well
conserved in both plants and animals, and are thought to be a vital and
evolutionarily ancient component of genetic regulation though they
appear to have evolved independently from the ancestral state in the
two kingdoms and to have different modes of action. miRNAs can be
carried by vectors from one cell to another and so may participate in
HGT.
 Transposable elements:
o Think of them as molecular parasites which may accidentally
create adaptive (or harmful) mutations and phenotypic
variations
o Transposons: produce special transposase enzymes that allow
it to insert copies of itself into various target sites in an
organism’s nucleus
Chapter 13: Genetic Variation in
Populations
Carl von Linné
(Carolus
Linnaeus)
(1707-1778)
Swedish



Bernard
Kettlewell
(1907-1979)
British

Popularized the binomial
nomenclature
The idea originated with Swiss
Botanist Gaspard Bauhin in 1623
in his Pinax Theatri Botanici
Attempted to classify the material
world as evidence of the power of
the Christian God with Systema
Naturae (1753)
performed extensive field studies
in Britain in the 1950s to test the
hypothesis that bird predators
were altering the frequencies of
the color morphs based on the
moths’ contrast to their
backgrounds, such as tree bark,
when they were at rest


Wilhelm
Weinberg
(1863-1937)
German

Godfrey H.
Hardy
(1877-1947)
English

William Ernest
Castle
(1867-1962)
American



Experiments: studies
demonstrated that native birds
did eat peppered moths. Release
and capture studies in two areas
indicated that peppered forms
survived in greater numbers in
unpolluted forests while melanic
forms survived in greater
numbers in soot polluted forests.
In his famous experiment, he
placed moths on dark and pale
tree trunks and showed that
background strongly influenced
moth survival against predation.
The Evolution of Melanism: a study
of recurring necessity; with special
reference to industrial melanism in
the Lepidoptera (1973)
Physician who independently
concluded that the original
proportions of the genotypes in a
population remain in equilibrium,
constant from generation to
generation as long as the five H-W
assumptions are met
Mathematician who
independently concluded that the
original proportions of the
genotypes in a population remain
in equilibrium, constant from
generation to generation as long
as the five H-W assumptions are
met
Geneticist who independently
concluded that the original
proportions of the genotypes in a
population remain in equilibrium,
constant from generation to
generation as long as the five H-W
assumptions are met
The first to use Drosophila
melanogaster in genetics
experiments
He trained Sewall Wright
A.T. Pietrewicz and
A.C. Kamil
?
?



Judith Hooper
(1949- )
American

Ronald A. Fisher
(1890-1962)
British




John Burdon
Sanderson
[J.B.S.] Haldane
(1892-1964)
British


Sewall Wright
(1889-1988)
American

1977- tested whether these choices by
moths were selectively advantageous
They trained blue jays to respond to slides of
moths by pecking a button for a food reward
whenever they spotted a moth
Results showed that blue jays spotted moths
less often on birch trees and especially when
a moth was oriented with its head up
Journalist that attacked Kettlewell in her
book Of Moths and Men but her book has
been dismissed by scientists for lack of
scientific understanding, prejudice and
careless journalism
Mathematician and geneticist who
combined Mendelian inheritance
with population genetics
noted that the greater the genetic
variation upon which selection for
fitness may act, the greater the
expected improvement in fitness
a founder of population genetics
and major contributor to the NeoDarwinian Modern Synthesis of
evolutionary theory based on
population genetics
he pioneered methods for
computing the distribution of gene
frequencies among populations as
a result of the interaction of
natural selection, mutation,
migration and genetic drift
Biologist and mathematician who
independently proposed (1928) a
similar hypothesis that conditions
on the primitive Earth favored
chemical reactions that synthesized
organic compounds from inorganic
precursors: biopoiesis from the
“primordial organic soup”
a founder of population genetics
and major contributor to the NeoDarwinian Modern Synthesis of
evolutionary theory based on
population genetics
Mathematician and geneticist who
combined Mendelian inheritance
with population genetics





Peter R. Grant PRB (1936- ) & British
& B. Rosemary BRG (1936- )
Grant


a founder of population genetics
and major contributor to the NeoDarwinian Modern Synthesis of
evolutionary theory based on
population genetics
He discovered the inbreeding
coefficient and methods of
computing it in pedigree animals
he pioneered methods for
computing the distribution of gene
frequencies among populations as
a result of the interaction of
natural selection, mutation,
migration and genetic drift
introduced the concept of fitness
landscapes or adaptive landscapes
which are used to visualize the
relationship between genotypes
and reproductive success
proposed the Shifting Balance
Theory, that genetic drift can be
quite important in changing allele
frequencies among populations
when the effective size of the
population is small
conducted long-term studies of
selective changes in Darwin’s
finches on the Galapagos Islands
“The population tracks a moving
peak in an adaptive landscape
under environmental fluctuations,
and there is more than one
individual fitness optimum within
the range of phenotypes in the
population.”
Concepts
Bernard Kettlewell- field studies in Britain in the 1950s tested
the hypothesis that bird predators were altering the frequencies
of the color morphs based on the moths’ contrast to their
backgrounds (tree bark) when they were at rest.
Experiments: studies demonstrated that native birds did
eat peppered moths. Release and capture studies in two areas
indicated that peppered forms survived in greater numbers in
unpolluted forests while melanic forms survived in greater
numbers in soot polluted forests. In his famous experiment, he
placed moths on dark and pale tree trunks and showed that
background strongly influenced moth survival against predation.
His career’s work was summarized in The Evolution of
Melanism: a study of recurring necessity; with special reference to
industrial melanism in the Lepidoptera (1973).
 Without variation there would be no evolutionary change
 Mutation provides one source of genetic variation
 Mutation is not entirely random: some parts of the genome are
more susceptible to mutation than are others
 The large amount of polymorphism at gene loci provides a
much greater source of genetic variation than do the relatively
few new mutations that arise each generation.
 At the population level, allele frequency provides a measure of
genetic variations
 Genetic drift within a population and gene flow between
populations provide sources of genetic variation
 Genetic variation provides the row material enabling
evolutionary change in response to natural selection
 Large-scale geographical patterns of species distribution can be
determined using the genetic history of populations
Mutation - any change in the cell’s DNA base sequences
Mutation rate – the probability that a gene will mutate when the cell
divides
Contributions to enhanced variation at the population level:
- Mutation
- Random drift in gene frequencies within a population
- Gene flow between populations
Quantitative trait loci (QTL) - regions of that contain blocks of genes,
often influencing characters that show continuous variation, such as height
or weight
Contributions to the maintenance of genetic diversity (genetic
polymorphism) within populations:
-randomness of mutation
-variation in mutation rates among genes and among species
-frequency of alleles in populations
-ability of DNA to repair itself
Mutations supply an important source of variation upon which selection acts
and which selection incorporates into evolutionary change.
Optimal mutation rates are advantageous.
Hot Spots of Mutation - specific nucleotide sequences that are the sites
where the nucleotide change is less readily repaired or compensated for than
is a sequence change at another site
Mutation rates are not only low, they are not constant. As with other
essential traits, mutation rates seem mostly selected for optimum values,
balancing on the delicate adaptive line between retaining prevailing adaptive
features yet facilitating the origin of new features.
A remarkable way in which some organisms accumulate mutations without
experiencing immediate effects is to bind their gene products with heat
shock proteins.
Heat shock proteins (hsp) - molecular chaperones that help other proteins
maintain their normal 3D conformation during polypeptide translation at the
ribosome and prevent them from being degraded.
• Heat shock proteins may be disabled in new stressful environments
– dramatic change in temperature
– dramatic change in pH
– dramatic change in salinity
Evolutionary potential and genetic variation are two sides of the same
evolutionary coin.
Genetic polymorphism - The presence of two or more alleles, each at a
frequency of 1% or more, at a gene locus in the gene pool of a deme or of an
entire species over a succession of generations. Genetic polymorphism
provides a much greater source of genetic variation with the potential for
evolutionary change than do the relatively few new mutations that arise in
each generation.
Genetic polymorphism is called balanced polymorphism when the
persistence of the different alleles cannot be accounted for by mutation
alone. In such cases, selection and/or migration are often the cause.
Researchers may focus on obvious phenotypic changes such as Mendel
observed, called discontinuous variation, evidenced in characters that form
a few distinct phenotypic classes, e.g., red, pink, or white flower color; or on
small changes or continuous variation, evidenced in characters for which
the plots of the distribution of the variation form a bell-shaped curve or
normal distribution, e.g., height or body mass of most animals or plants.
Enzyme polymorphism-Change in catalytic ability due to change in
temperature, osmotic environment, pH,
DNA sequence polymorphism-Changes in bases, codons, introns, exons,
etc.
Polygenic inheritance, also known as quantitative or multifactorial
inheritance refers to inheritance of a phenotypic characteristic (trait) that is
attributable to two or more genes, or the interaction with the environment, or
both; do not follow patterns of Mendelian inheritance (separated traits).
Instead, their phenotypes typically vary along a continuous gradient depicted
by a bell curve
Population- group of individuals of the same species that can interbreed
with one another
Polymorphism – many traits display variation within a population
– Due to 2 or more alleles that influence phenotype
Polymorphic gene- 2 or more alleles
Monomorphic – predominantly single allele
Single nucleotide polymorphism (SNPs)
– Smallest type of genetic change in a gene
– Most common – 90% of variation in human gene sequences
Balanced polymorphism- the persistence of two or more different genetic
forms through selection
Quantitative trait loci (QTL) – all of the genes (alleles) in a particular
region of a chromosome that affect a quantitative aspect of the phenotype
QTL analysis enables us to isolate suites of genes acting on particular parts
of the phenotype at particular stages in ontogeny and to determine their
relative affects.
In the 1930’s, it became accepted that:
1.) Evolution is a population phenomenon that
2.) can be represented as a change in gene (now allele) frequencies
because of the action of various natural forces such as mutation,
selection and genetic drift, and that
3.) these changes can lead to differences among populations, species, and
higher clades. This population genetics view of evolution became
known as the neo-Darwinian theory with its emphasis on the
frequency of genes in populations as the basis of evolutionary change.
Population genetics deals with genes as alleles and gene frequencies as
allele frequencies.
Allele frequencies (the frequencies of individual alleles) and the gene pool
(all the alleles of all individuals in the population) are two major attributes
of a population.
The Hardy-Weinberg Equtlibrium states that original
proportions of the genotypes, and therefore the gene pool allele
frequencies, in a population remain constant from generation to
generation as long as the five H-W assumptions are met:
the five H-W assumptions that need to be met are a (1) large (2) random
breeding population undergoing (3) no mutation, (4) no selection and (5)
no migration of genes or individuals
The Hardy-Weinberg Equations
p + q= 1
and
p2 + 2pq + q2 = 1
p = the frequency of the first or dominant allele
q = the frequency of the second or recessive allele
p2 = individuals homozygous for first or dominant allele
2pq = individuals heterozygous for the alleles
q2 = individuals homozygous for second or recessive allele
Hardy-Weinberg principle –The conservation of gene (allelic) and
genotype frequencies in large populations under conditions of random
mating and in the absence of evolutionary forces, such as selection,
migration, and genetic drift, which act to change gene frequencies.
The simplifying assumptions for the H-W Equilibrium are:
1) diploid organisms
2) sexual reproduction
3) generations are non-overlapping
4) equally viable genotypes
The Hardy-Weinberg principle is the founding theorem of population
genetics.
Population – a group of sexually interbreeding or potentially interbreeding
individuals
Nonrandom Mating- mating between specific genotypes shifts genotype
frequencies
– Assortative Mating: does not change frequency of individual
alleles; increases the proportion of homozygous individuals
– Disassortative Mating: phenotypically different individuals
mate; produce excess of heterozygotes
Deme – local population of organisms of one species that interbreed with
one another more than they do with other demes and share a distinct gene
pool. The considerable genetic variability in human groups shows that
populations of modern humans are demes.
Genetic load - the extent to which a population departs from an optimal
genetic constitution; the loss in average fitness of individuals in a
population because the population carries deleterious alleles or
genotypes.
Genetic death - can be classified as either sterility, inability to find a mate,
or by any means that reduces reproductive ability
A population may receive alleles from a nearby population in a process
known as gene flow or sometimes as migration because individuals,
gametes, or even individual genes, move from population to population,
taking their alleles with them.
At least three factors have an impact on the recipient population:
1. the difference in gene frequencies between the two populations
2. the proportion of migrating genes incorporated into each
generation; and
3. the pattern of gene flow, whether occurring once or continually
over time.
4. Gene flow-a movement of genes from one population to another
Gene flow-a movement of genes from one population to another
Genetic drift – (Also known as allelic drift or the Sewall Wright effect)
variation in the relative frequency of different genotypes and allele
frequencies in the gene pool, usually in a small population, owing to the
chance disappearance of particular alleles as individuals die or do not
reproduce; random fluctuations in allele frequencies that arise as a
consequence of sampling error in mating opportunities, usually in small
populations; in large populations, drift is countered by selection; drift may
increase the chances for speciation or extinction of the population
Effective population size (Ne) – formula for calculating the number of
parents who actually contribute offspring to the next generation.
(Ne) = (4NfNm/(Nf+Nm) where Nf in the number of female parents and Nm is the number
of male parents. Ne is the number of parents who actually contribute offspring to the next
generation.
We can conclude that genetic drift increases with variation between
populations, but on the average, not in any particular direction.
R.A. Fisher formulated a fundamental theorem that essentially states that the
greater the genetic variation upon which selection for fitness may act, the
greater the expected improvement in fitness.
Variation itself is subject to selection, and so the propensity to vary
(variability) is an important attribute of organisms.
Phylogeography – The study of the evolutionary processes regulating the
geographic distributions of lineages/groups by reconstructing genealogies of
individual genes, groups of genes or populations.
The neo-Darwinian theory
1. Evolution is a population phenomenon
2. Evolution when there is a change in gene (now allele) frequencies
in a population because of various natural forces such as mutation,
selection and genetic drift
3. These changes in allele frequencies lead to differences among
populations, species, and higher clades
4. This population genetics view of evolution became known as neoDarwinian theory with its emphasis on the frequency of genes in
populations
Five agents of Evolutionary Change:
1. Gene Flow
2. Selection
3. Nonrandom mating
4. Genetic drift
5. Mutation
Founder Effect - A situation encouraging genetic drift that occurs when a
few individuals (founders) derived from a large population begin a new
colony. Since these founders carry only a small fraction of the parental
population’s genetic variability, different gene frequencies can become
established in the new colony.
Bottleneck Effect – A situation encouraging genetic drift that occurs when a
population is reduced in size and later expands in numbers. Since the
survivers carry only a small fraction of the parental population’s genetic
variability, different gene frequencies can become established in the
surviving population.
Shifting Balance Theory- proposed by Sewall Wright in 1931
1. Genetic drift, acting on genetic variation at various loci, allows a
number of demes to change their allele frequencies. As fitness
changes such demes are modeled as moving across non-adaptive
2.
3.
4.
5.
6.
valleys to different parts of an adaptive landscape, a model
discussed in Chapter 15.
Selection pushes some of these demes up the nearest available
adaptive peak by changing allele frequencies even further.
Variation at other loci provides further opportunity for genetic drift
to move a population to a higher adaptive peak.
A deme that has a high fitness coefficient tends to displace other
demes of lower fitness by expanding in size or dispersing outward
and changing the genetic structure of other demes through
migration.
Environmental change such as a stream of seismic earthquakes,
can act on populations by changing the environment to which
populations must adjust or perish. Channeling selection in new
directions encourages populations to continually shift their genetic
structures. “The population tracks a moving peak in an adaptive
landscape under environmental fluctuations and there is more than
one individual fitness optimum within the range of phenotypes in
the population.” –P.R. and V.R. Grant
Selection, time, and genetic accident are needed to achieve the
most optimum genotypes, although genetic loads and changes in
the environment can oppose achieving the optimal genotype.
Red Queen Hypothesis - the hypothesis that adaptive evolution in one
species of a community causes a deterioration of the environment of other
species. As a consequence, each species must evolve as fast as it can in order
to continue to survive. It comes from Lewis Carroll's Through the Looking
Glass in which the Red Queen said to Alice, “Now, here, you see, it takes all
the running you can do, to keep in the same place.”
Chapter 14: The Biology of
Populations
Robert H.
MacArthur
(1930-1972)
American

leading 20th century ecologist who
moved the study of ecology from a


Edward O.
Wilson
(1929- )
American




Richard
Lewontin
(1929- )
American


Concepts
descriptive to an experimental
discipline
Did research on niches and
foraging behaviors
The Biology of Populations (1966)
and Geographical Ecology (1972)
and co-author of The Theory of
Island Biogeography (1967)
One of America’s major 20th
century evolutionary biologists
A specialist in ants and social
insects who became a major
theorist of animal social behavior
and later a major advocate for
understanding and protecting
biodiversity
Founder of a subdiscipline:
Sociobiology: The New Synthesis
(1975)
The Diversity of Life (1992),
Consilience: The Unity of
Knowledge (1998), On Human
Nature (2004) and The Social
Conquest of Earth (2013) and coauthor of The Theory of Island
Biogeography (1967)
evolutionary biologist who
captured the essence of the niche
and of the evolutionary
relationships of an organism to its
(self-made) environment in his
book, The Triple Helix: Gene,
Organism, and Environment
(2000)
pioneered the combination of data
from molecular biology and
population genetics mathematics
and statistics
Co-evolution is the set of mutual evolutionary influences shared
between two or more species occupying a common habitat; possible
when there is some overlap among the niches of two or more species;
when two (or more) species: (1) exert selective pressures on each other,
and (2) evolve in response to each other
Because each species is evolving in response to the other, one important
feature of co-evolution is that the:
• Selective environment is constantly changing
• Also, selective pressures will be strongest when there is a close
ecological relationship
• Species do not evolve in a vacuum
• Darwin emphasized competition between members of the same
species for limited resources
• Ecologists emphasize the competition between different species
for the same limited resources
• Co-evolution includes competition for both abiotic and biotic
resources
Co-Evolution with Pathogens:
Thomas Austin’s rabbits population boom; introduction of
myxomavirus; mortality rates in rabbits about 90%; now rabbit
population is smaller but virus only has about 40% mortality rate
because of surviving resistant rabbits and evolution of less virulent
pathogen
Definitions of Niche

Where an organism is found and what it does there
• The role of an organism in an ecosystem
• The role of a species within a community
• All the functional roles of an organism in a biological community
• A unique ecological role of an organism in a community
• The environmental habitat of a population or species, the
resources it uses and its interactions with other organisms
• The status of an organism within its environment and community
as it affects the survival of the species
• The role or functional position of a species within the community
of an ecosystem
• The physical and functional role of an organism within an
ecosystem
Competition arises when two groups depend on the same limited
environmental resources so that each group causes a reduction in the
other’s numbers, often with important ecological or behavioral
consequences.
• Three consequences of competition are outlined below:
o Resource Partitioning:
 The situation in which competing groups of
organisms minimize the harmful effects of
direct competition by using different aspects of
their common environmental resources
o Character Displacement:
 Phenotypic differences accompany resource
partitioning among coexisting groups
o Competition Exclusion:
 The principle that two species cannot continue
to coexist in the same environment (niche) if
they use it in the same way.
Important ecological relationships that give rise to coevolution:
1. Predator and Prey – predators can reduce the possibility of a
dominant species reaching its carrying capacity; prey species
crash first, then predators starve
Defenses against Predators:
 Camouflage
 Startle Responses - When a prey species can change its
appearance suddenly and therefore frighten or distract a
predator; example include wing or body displays that reveal
eyespots, or other color changes from behavior that confuse
the predator, such as flicker fusion when a striped snake
starts moving and the stripes become a blur.
 Flash Coloration - a patch of bright contrasting color that is
revealed, e.g., by unfolding wings, apparent only during
motion on an otherwise neutrally tinted animal and that is
believed to distract the attention of predators who lose
sight of the prey when it comes to rest and the flash color
patch is obscured
 Aposematism - was a new term coined by Edward Bagnall
Poulton for Alfred Russel Wallace's concept of warning
coloration. It describes a family of antipredator adaptations in
which a warning signal is associated with the unprofitability of a
prey item to potential predators. Aposematism always involves an
advertising signal. The warning signal may take the form of
conspicuous animal coloration, sounds, odors or other
perceivable characteristics. Aposematic signals are beneficial for
both the predator and prey, since both avoid potential harm
 Aposematism is exploited in Müllerian mimicry, where species
with strong defenses evolve to resemble one another. By
mimicking similarly colored species, the warning signal to
predators is shared, causing them to learn more quickly at less of
a cost to each of the species.
 Warning signals do not necessarily require that a species
actually possesses chemical or physical defenses to deter
predators. Mimics such as the nonvenomous California mountain
kingsnake (Lampropeltis zonata), which has yellow, red, and black
bands similar to those of highly venomous coral snake species,
have essentially piggybacked on the successful aposematism of
the model. The evolution of a warning signal by a mimicking
species that resembles a species that possesses strong defenses is
known as Batesian mimicry.
 Aposematic Behaviors
 Aposematic Colors
 Toxicity
 Mimicry: In evolutionary biology, mimicry is a similarity of one
organism, usually an animal, to another that has evolved because
the resemblance is selectively favored by the behavior of a shared
signal receiver that can respond to both. Mimicry may evolve
between different species, or between individuals of the same
species. Often, mimicry evolves to protect a species from
predators, making it an antipredator adaptation. The
resemblances that evolve in mimicry can be in appearance,
behavior, sound or scent. Mimicry may be to the advantage of
both organisms that share a resemblance, in which case it is a
mutualism, or mimicry can be to the detriment of one, making it
parasitic or competitive.
 Mimicry occurs when a group of organisms, the mimics, evolve
to share perceived characteristics with another group, the
models. The evolutionary convergence between groups is driven
by the selective action of a signal-receiver or dupe. Birds, for
example, use sight to identify palatable insects, whilst avoiding
the noxious ones. Over time, palatable insects may evolve to
resemble noxious ones, making them mimics and the noxious
ones models. In the case of mutualism, sometimes both groups are
referred to as "co-mimics".
 In its broadest definition, mimicry can include non-living models.
The specific terms masquerade and mimesis are sometimes used
when the models are inanimate. For example, animals such as
flower mantises, planthoppers and geometer moth caterpillars
that resemble twigs, bark, leaves or flowers practice masquerade.
Some authors would consider this mimicry, others would not.
Many animals bear eyespots, which are hypothesized to resemble
the eyes of larger animals. They may not resemble any specific
organism's eyes, and whether or not animals respond to them as
eyes is also unclear. Nonetheless, eyespots are the subject of a rich
contemporary literature.
 The model is usually another species, except in automimicry,
where members of the species mimic other members, or other
parts of their own bodies, and in inter-sexual mimicry, where
members of one sex mimic members of the other. It is often
thought that models must be more abundant than mimics, but it
has been shown that this is not necessarily a requirement.
 Though visual mimicry through animal coloration is most obvious
to humans, other senses such as olfaction (smell) or hearing may
be involved, and more than one type of signal may be employed.
Mimicry may involve morphology, behaviour, and other
properties. In any case, the mimetic signal always functions
because it resembles that of another organism. In evolutionary
terms, this phenomenon is a form of co-evolution. It can involve
an evolutionary arms race if mimicry negatively affects the model,
and the model can evolve a different appearance from the mimic.
Mimicry should not be confused with other forms of convergent
evolution, which occurs when species come to resemble each
other by adapting to similar lifestyles that have nothing to do with
a common signal receiver.
 Mimics may have different models for different life cycle stages, or
they may be polymorphic, with different individuals imitating
different models. Models themselves may have more than one
mimic, though frequency dependent selection favours mimicry
where models outnumber mimics. Models tend to be relatively
closely related organisms,[ but mimicry of vastly different species
is also known. Most known mimics are insects, though many other
animal mimics are known. Plants and fungi may also be mimics,
though less research has been carried out in this area.
 Ingestion Defenses: Spikes & Horns & Thorns - a tough,
sharp, protective defensive external surface projection to
reduce the desire of biting organisms to bite into the target
organism's tissues; it includes spikes, horns, thorns, spines,
etc. (They may serve other adaptive purposes as well.)
 Ingestion Defenses: Fangs & Tusks - sharp teeth which
may be used to discourage predators from biting a target
organism. (They may serve other adaptive purposes as
well.)
 Ingestion Defenses : Armor - a tough, protective defensive
external covering to reduce the penetration of biting
organisms into the target organism's tissues; it includes cell
wall material, shells, exoskeletons, dermal thickenings,
bones and bony plates, etc.
 Ingestion Defenses: Toxic Chemicals
2. Parasite and Host
3. Mutualists
4. Competitors(as described above)
 Resource Partitioning
 Character Displacement
 Competitive Exclusion
Detritivores – eukaryotes (certain protistans and animals) which use
for the mechanical breakdown (chewing) to feed on dead organic
material (detritus)
Decomposers – prokaryotes (certain bacteria) and eukaryotes (certain
protistans and fungi) which use externally secreted enzymes for the
chemical breakdown (chemical digestion) to feed on dead organic
material (detritus)
bone morphogenic protein 4 (Bmp-4) – a homeobox (hox) gene; its expression is a major contributor
to jaw size and tooth development in fish as well as beaks in birds; controls dorsi-ventral
differentiation of mesodermal tissues in other animals
Change in expression of a single gene explains why significant
morphological change can occur in just a few generations, as
observed in the Darwin’s finches.
phenotypic plasticity - facultative ability of a single genotype to
produce more than one phenotype:
• The variation in phenotype (for a given genotype) which
occurs due to the influence of environmental factors.
• Can represent the small and sometimes trivial differences
which we observe in identical twins (perhaps a taller, more
muscular twin works out more or has better diet than other
twin).
• Represents the sorts of regular changes observed when
individuals of the same genotype develop or behave
differently when they live in different environments
• One phenotype may be a negative consequence of an
inadequate environment.
• Phenotypic plasticity can evolve like any other potentially
adaptive trait
Examples of Phenotypic Plasticity
• Interactions between individuals of predator and prey species of
rotifers (Phylum Rotifera); when the predator is present, the prey
species detects predator chemicals and grows defensive spines
• Daphnia species respond to predators; individual water fleas have
the potential to grow a “helmet” and longer spine when exposed
to chemicals from various of their natural predators (midge larvae
and fish); the genetic potential was already present in the Daphnia
genome, but it requires the action of the predator’s chemical cues
to activate the genes for the altered morphology
• In spadefoot toads: when crowded, large cannibalistic morphs
develop which prey on the normal tadpoles
• Moth Nemoria arizonaria: something in the oak plant tissue
consumed by the caterpillar drives the change in morphology
(spring caterpillar morph resembles blossom of tree, summer
morph resembles twig on tree)
A survivorship curve is a graph showing the number or proportion of
individuals surviving to each age for a given species or group (e.g. males
or females). Survivorship curves can be constructed for a given cohort
(a group of individuals of roughly the same age) based on a life table.
There are three generalized types of survivorship curves:
Type I survivorship curves are characterized by high age-specific
survival probability in early and middle life, followed by a rapid decline
in survival in later life. They are typical of species that produce few
offspring but care for them well, including humans and many other
large mammals.
Type II curves are an intermediate between Types I and III, where
roughly constant mortality rate/survival probability is experienced
regardless of age. Some birds and some lizards follow this pattern.
In Type III curves, the greatest mortality (lowest age-specific survival)
is experienced early in life, with relatively low rates of death (high
probability of survival) for those surviving this bottleneck. This type of
curve is characteristic of species that produce a large number of
offspring (see r/K selection theory). This includes most marine
invertebrates. For example, oysters produce millions of eggs, but most
larvae die from predation or other causes; those that survive long
enough to produce a hard shell live relatively long.
The number or proportion of organisms surviving to any age is plotted
on the y-axis, generally with a logarithmic scale starting with 1000
individuals, while their age, often as a proportion of maximum life span,
is plotted on the x-axis.
Life history strategies occur along a continuum characterized as r- and
K-selection
• Where individual species fall on the r-K continuum is largely
determined by the environment in which they live and the
environment they live in is influenced by their presence and life
styles
• McArthur & Wilson developed an elegant system for describing
the stability and age distribution of natural populations known as
“r/K selection”
The variables r and k in r-and k-selection come from the logistic
equation for population growth

I = rN (K-N / K) calculates the annual growth of a population
 I = the annual increase for the population,
 r = the annual growth rate: (birth rate + immigration
rate) – (death rate + emigration rate)
 N = the population size
 K = the carrying capacity: (max density at which
population can exist in given environment)

Habitat
Succession
Stage
Population
Growth
Potential vs.
Extinction
Potential
Competition
Among
Individuals
Life History
Traits and
Mortality
r-Strategist
unstable, variable,
ephemeral, unpredictable
early succession stage,
“weedy” colonists with good
dispersal abilities
maximized, exponential;
less vulnerable to extinction
K- Strategist
long term stability
variable, reduced;
resources exceed demand;
weak competitors
precocial young, early
maturity onset, shorter
generation time; mortality
continual and intense,
resources in short supply;
good competitors
altricial young, late maturity
onset, longer generation
time; mortality low, more
constant and predictable
climax community, reduced
dispersal abilities
low, at equilibrium;
vulnerable to extinction
high, variable and
unpredictable
small
high
Body Size
Fecundity
and
Dispersal
Rates
Resource
high but individual
Allocation to offspring are of low quality;
Reproduction reduced parental care
/ Parental
Care
Life Strategy
many offspring, few
Trade Off
survive to reproduce
larger
low
low but individual offspring
are of high quality;
increased parental care
few offspring, most survive
to reproduce
Climax community – stable community; the final stage in an ecological
succession process, likely to persist for long periods of time; its
composition will depend on location, climate, and other abiotic factors;
K-selected species will predominate in these communities over time.
The Red Queen Hypothesis - the hypothesis that adaptive evolution in one
species of a community causes a deterioration of the environment of other
species. As a consequence, each species must evolve as fast as it can in order
to continue to survive. It comes from Lewis Carroll's Through the Looking
Glass in which the Red Queen said to Alice, “Now, here, you see, it takes all
the running you can do, to keep in the same place.” The Red Queen
Hypothesis is used to describe three ideas based on co-evolution
relationships or evolutionary arms races; one relating to extinction
probability, another to the value of sexual reproduction, the third to
host-parasite/pathogen relationships.
• The original idea, proposed by Leigh Van Valen in 1973, with the
paleontological perspective, is that co-evolution could lead to
situations for which the probability of extinction is relatively
constant over millions of years rather than being proportional to
the population's lifetime. In tightly co-evolved interactions, e.g.,
predator and prey, or host and parasite, the sudden evolutionary
change by one species could lead to the extinction of other species
and that the probability of such changes might be reasonably
independent of species age. This is the long term paleontological
macroevolutionary perspective.
• The other idea, advocated by W.D. Hamilton, among others, with
the neontological perspective, relates to the benefit of sexual
reproduction. This idea is that co-evolution, particularly in
evolutionary arms races between hosts and parasites, could lead
to sustained oscillations in genotype frequencies. As one
genotype of host is most susceptible, its most effective parasitic
genotype will prosper. However, this forms a selection pressure
to favor a resistant host. When that resistant host genotype
appears or merely increases in numbers, a new selection pressure
forms on the original parasite genotype, which is now less
infectious or virulent in the new host genotype. Thus, one host
genotype will replace a former one, only to be followed by parallel
replacement of genotype in the parasite. Sexually reproducing
species which allow recombination of alleles among different
individuals in their populations will have the potential for more
rapid evolutionary change, speeding up the oscillations in
genotypes of hosts and parasites, even if no new alleles arise in
either gene pool. This hypothesis can also explain the shift
between sexual and asexual modes of reproduction in species
capable of both forms of reproduction. This is the short term
neontological (living species) microevolutionary perspective.