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http://www.cdc.gov/swineflu/
Evolution and Population Genetics
SCBI 113 Essential Biology
Nuttaphon Onparn, PhD.
28 April 2009
Swine Flu (Influenza A: H1N1) Outbreak 2009
Source: WHO
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hemagglutinin , neuraminidase
Swine Influenza Virus (SIV)
Hybridziation, antigenic shift
3
http://en.wikipedia.org/wiki/File:Symptoms_of_swine_flu.svg
4
http://en.wikipedia.org/wiki/File:Flu_und_legende_color_c.jpg
Outline
• Evolution and population genetics
– Introduction
• National Science Museum
– Sue and Thai Dinosaurs Exhibition
– Evolution, species and speciation
– Population genetics
5
6
1
Sue the Tyrannosaurus rex (67-65 MYA)
7
Siamotyrannus isanensis (130 MYA)
9
8
Lucy the Australopithecus afarensis (3.2 MYA)
10
Bio-Geo Path at Mahidol, Payathai
11
Cenozoic Era display in Natural History Museum
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Mechanisms of Evolution
• Hawaiian Drosophila
Nothing makes sense in
biology, except in the light
of evolution.
– 500 described
species
– One fertilized female,
a single founder
– More species than
islands
(T. Dobzhansky, 1973)
• Island within island
– Keneshiro hypothesis
• Mating behaviour
plays role in
speciation.
15
Introduction
Kenneth Kaneshiro, Evolutionary biologist
16
Introduction
• Darwin introduces a revolutionary
theory
• Natural selection as evolutionary
process
– On the Origin of Species by Means of
Natural Selection (November 24, 1859)
– Population changes over time, certain
heritable traits can help organism leave
offspring than other.
• Species are descendants of ancestral species
• Natural selection as evolutionary process
• Evolutionary adaptation
– An accumulation of inherited characteristics that
enhance organisms’ ability to survive and reproduce
in specific environment.
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18
3
Introduction
• Evolution
– Descent with modification
– A change over time in the genetic
composition of a population
• Speciation: new species
– A gradual appearance of all of biological
diversity.
19
A marine iguana, well-suited to its rocky habitat in the Galapagos Islands.
Historical Context
20
Scala Naturae
• Darwinism
• The sacle of nature and classification
of species
– Timing and logic
– Resistance to the idea of evolution
– Aristotle (384-322 B.C.) →
• Western culture: Earth is a few thousand years
old, populated by unchanging organisms.
• Scala naturae (scale of nature)
• (linear)
– Carolus Linnaeus (1707-1778) →
• classify life’s diversity for the greater glory of
God.
• (nested)
21
22
Catastrophism
• Fossils, Cuvier and catastrophism
– Fossils
• Remains or traces of organisms from the past.
The historical context of Darwin’s life and ideas.
23
24
4
Catastrophism
• Fossils, Cuvier and catastrophism
– Paleontology
• The study of fossils developed by Georges
Cuvier (1769-1832)
• Catastrophism
– Not believe in gradual evolution, strata boundaries
came from catastrophism.
– Sudden and violent changes (flood or drought) that
can destropy many species.
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Gradualism and Uniformitarianism
• Theories of Gradualism
– Change can take place by the cumulative
effect of slow, but continuous process.
Fossils from strata of sedimentary rock: The Colorado river and the Grand Canyon.
27
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Lamarck’s Theory of Evolution
Gradualism and Uniformitarianism
• Jean-Baptiste de Lmarck
• Uniformitarianism
– Evolutionary change explains the fossil record
and organisms’ adaptations to their
environments.
– James Hutton and Charles Lyell →
– Geological processes are operating today
as in the past, at the same rate.
• Darwin thought that similar slow process could
act on organism and produce changes as well.
• Changes occur, but no extinction. Species only
transformed.
– How does evolution occur?
• Use and disuse
• Inheritance of acquired characteristics
– Innate drive
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30
5
Darwin’s Research
• The Origin of Species
– Species change through natural selection
• Darwin
– Shrewsbury (western England)
– University of Edinbrugh (medicine)
– Cambridge University (clergyman)
• John Henslow (botanist)
• Robert FitzRoy (captain of HMS Beagle)
Acquired traits cannot be inherited: the bonsai.
31
The Voyage of the Beagle
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The Voyage of the Beagle
• What did Darwin find?
• What did Darwin find?
– Various adaptation of plants and animals
– Fossils were distinct, but resemble those living
species of the continent.
– Ecological diversity, from grassland to high
mountain
– Geologic processes can change the landscape
• Principles of Geology (Chales Lyell, 1830)
– South America temperate species are resembled
species in the tropic, rather than Europe
temperate species.
– Galapagos island species
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The voyage of HMS Beagle
6
Darwin’s Focus on Adaptation
Darwin’s Focus on Adaptation
• Adaptation and speciation
• The origin of species
– 1840s
– Could a new species arise from an
ancestral form by the gradual
accumulation of adaptations to a different
environment?
• major features done, Darwin was in poor
health.
– 1844
• the long essay was written but unpublished.
• Galapagos finches
– 1858
– Their beaks and behaviours are adapted to specific
food found on their specific islands.
• Alfred Russel Wallace wrote to Darwin
– 1859
• Darwin published “The Origin of Species”
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The Origin of Species
• Descent with modification
– Darwin’s view of life
– Tree of life
• Elephant evolution
– Linnaeus taxonomy
• Reflect the branching history of the tree of life
as species descended from their common
ancestors.
Beak variation in
Galapagos finches
40
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Descent with modification: evolutionary tree of elephant
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7
Observations and Inferences
• Observations
Observations and Inferences
• Inference
• Population would increase exponentially if all
individual reproduced successfully. (after
Thomas Malthus, 1798)
• But, populations tend to remain stable.
• Resources are limited
– Only a fraction survive as many struggled
for existence.
• Members of species vary
• Much of variations can be inherited (artificial
selection in agriculture)
43
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Observations and Inferences
• Inference
– Some traits give more fitness to organism
(survive and reproduce)
– Unequal fitness lead to gradual change in
a population.
45
Overproduction of offspring
46
Variation in population
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Artificail selection
8
Natural Selection
Natural Selection
• Definition
• Effects
– Natural selection is the differential
success in reproduction that results from
the interaction between individuals that
vary in heritable traits and their
environment.
– Over time, natural selection can increase
the adaptation of organisms to their
environment.
• If the environment change or individual move
to new habitat, natural selection could
sometimes give rise to new species.
• Differential success in reproduction
– The unequal ability of individuals to survive and
reproduce.
49
50
Natural Selection
• Unit of evolution
– A population is the smallest unit that can
evolve.
• Natural selection occurs through interaction
between individual and environment, but
individual do not evolve.
• Population
Camouflage as an
example of
evolutionary
adaptation
– A group of interbreeding individuals belonging to a
particular species and sharing a common
geographic area.
51
Natural Selection
52
Natural Selection
• Measuring evolution
• Life as Darwin see it
– Relative proportions of heritable variations
in a population over a succession of
generations.
53
– Life evolve through gradual accumulation
of small changes.
• Natural selection operates in various contexts
over time as can be seen in geological
evidence and the entire diversity of life.
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9
Differential Predation and Guppy Population
Differential Predation and Guppy Population
• Guppies (Poecilia reticulata)
• Guppies (Poecilia reticulata)
– Observation
– Experimentation
• Different average age and size at sexual
maturity.
• Correlation with type of active predator.
• Transplantation experiment
– Move guppies from pike-cichlid pool to killifish pool
(has no guppy prior the experiment)
– Small killifish → prey on juvenile guppies
– Pike-cichlid fish → prey on mature guppies
» Guppies with pike-cichlid reproduce at younger
age and are smaller at maturity.
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The Evolution of Drug-Resistant HIV
• Human Immunodeficiency Virus (HIV)
– The drug 3TC interfere with reverse
transcriptase. 3TC is cytosine analog.
– Some virus has reverse transcriptase that
can distinguish 3TC and normal C.
• This variation replicate slower than normal
virus.
• With 3TC, this variant replicate bettern than
normal virus.
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The Evolution of Drug-Resistant HIV
• Human Immunodeficiency Virus (HIV)
Natural Selection
• Two key points
– Drug-resistant pathogen can spread
quickly in the present of strong selective
force.
– Natural selection is a process of edition
not creation.
– Natural selection depends on time and
place.
• Adaptive in one situation become maladaptive
in other situations.
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62
Evidence of Evolution
• Evolution can help answer questions
– Why certain characteristics in related species
have an underlying similarity even though they
may have very different function.
• Homology
– Anatomical homologies
• Comparative embryology
– Molecular homologies
• Biogeography
• The fossil record
63
64
Evolution of drug resistance in HIV.
Homology
Homology
• Homology
• Homology
• Homologous structure
– Similarity resulting from common
ancestry.
– Anatomical homologies (comparative
anatomy)
– Variation on a structural theme that was present in
their common ancestor.
– Vestigial organs
» Remnants of structures that served important
functions in the organism’s ancestors.
• Comparison of body structures between
species.
• Comparative embryology
– The comparison of early stages of animal
development, not visible in adult organisms.
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Homology
• Homology
– Molecular homologies
• Similarity at the molecular level. All forms of
life use the same genetic machinery of DNA
and RNA.
• Many share genes (bacteria vs human)
– Homologies and the tree of life
• Molecular homology can date back to the
ancestral past.
• Some homologies evolved just recently
(tetrapods), 5-digit limbs → nested pattern.
• Organisms evolved from a common ancestor.
67
Mammalian forelimbs: homologous structure
68
Anatomical similarities in vertebrate embryos
69
Comparision of a protein found in diverse vertebrates
70
Biogeography
• Biogeography
– The geographic distribution of species.
• Closely related species tend to be found in the
same geographic region.
• Distant region with same ecological niche
occupied by different species (sometimes look
similar).
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12
Biogeography
• Biogeography
• Australia
– Australian marsupials have eutherian lookalike. (i.e.
sugar glider and flying squirrel).
– Convergent evolution (not homologous)
• Endemic
– Species that found no where else (Galapagos,
Hawaii)
Different geographic regions,
different mammalian brands
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The Fossil Record
• The fossil record
– The Darwinian view of life predicts that
evolutionary transitions should leave
signs in the fossil record.
•
•
•
•
Ape and Human fossils
Dinosaur and bird fossils
Terrestrail mammal and whale fossils
Not so fossil: prokaryote and eukaryote
A transitional
fossil linking
past and
present
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13
Darwin’s Theory of Evolution
Fact or Theory?
• Does Darwinian view of lfie a fact or a
theory?
• It can explains so many different kinds
of observations.
– As can be seen from various evidence, it is a fact.
– Homologies match patterns in space
(biogeography) and time (the fossil
record).
• The different between theory and fact or
hypothesis.
– With many observation and data, hypothesis
become theory.
– Natural selection can explain how similar
adaptations can evolve independently
(convergent evolution, e.g. sugar glider
and flying squirrels)
• Is natural selection the only evolutionary
mechansim?
79
– No. Other factors have been found to play
important roles.
80
Outline
• Key concepts
– Biological species concept
– Reproductive isolation
– Speciation
The Origin of Species
• Allopatric speciation
• Sympatric speciation
The definition of species and
speciation process
– Macroevolution and many speciation
events
82
Mystery of Mysteries
Mystery of Mysteries
• Darwin’s diary
• Evolutionary changes
– Galápagos Island
• “Both in space and time, we seem to be
brought somewhat near to that great fact – that
mystery of mysteries – the first appearance of
new beings on this earth.”
• Speciation
– The origin of new species
– The source of biological diversity (species
diversity)
83
– Microevolution
• Changes confined to single gene pool
(at species level)
– Macroevolution
• Evolutionary changes above species
level
– Evolutionary novelties (e.g. feathers
separate birds from dinosaurs)
84
14
Two patterns of
evolutionary
change
How would you
explain the origin of
flightless birds?
The flightless cormorant (Nannopterum harrisi), one of many new species
85
that have originated on the isolated Galápagos Islands.
86
What is Species?
Patterns of Evolutionary Changes
• Anagenesis
• Species
– Ana=new, genos=race (new race)
– One species transform to another species.
– Number of species not increase
– Latin word, species=kind or appearance
• Real or artificial?
• Cladogenesis
– Klados=branch, genos=race (branching evolution)
– Gene pool split, give rise to one or more new
species
– Number of species increase
• Biological diversity
– Real entity as species can recognize its
own species.
– Higher taxonomic levels are artificial.
• Continuous or discrete
– Discrete (morphologically distinct species)
– Cladogenesis
87
The Biological Species Concept
• Biological species concept (BSC)
88
The Biological Species Concept
• Limitations of the BSC
– Ernst Mayr (1942)
– Members of the same species are
reproductively compatible.
• A species as a population or group of
populations whose members have the potential
to interbreed in nature and produce viable,
fertile offspring, but are unable to produce
fertile offspring with other populations.
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– Fossil (extinct species)
– Asexual organisms
– No information of reproduction =
inconclusive
– Has no potential to interbreed
(geographically isolated)
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Reproductive Isolation
• Reproductive isolation
• Factors that prevent members of two
species producing viable, fertile hybrid
offspring.
Similarity between different species
(Left) The eastern meadowlark
(Sturnella magna)
(Right) The western meadowlark
(Sturnella neglecta)
Both are distinct species, their song
and behaviour are different prevent
interbreeding if they meet in the wild.
– Many barriers can work together.
– Gene flow restriction
Diversity within a species
All human (Homo sapiens) can
interbreed.
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Reproductive Isolation
Reproductive Isolation
– Prezygotic barriers (before the hybrid
zygotes are formed)
– Postzygotic barriers (after the hybrid
zygotes are formed)
•
•
•
•
•
Habitat isolation
Temporal isolation
Behavioural isolation
Mechanical isolation
Gametic isolation
• Reduced hybrid viability
• Reduced hybrid fertility
• Hybrid breakdown
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Postzygotic isolation
Prezygotic isolation (cont)
Prezygotic isolation
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Other Species Concepts
Other Species Concepts
• Morphological species concept
• Paleontological species concept
– Similarity between members of species is
greater than with other species.
– Morphological discrete characters found
from fossils.
• Good for both sexual and asexual species;
taxonomists use this for ages.
• Bad for its subjectivity, lack of reproductive
isolation data
• Good for fossil identification
• Bad for its lack of reproductive isolation data
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Other Species Concepts
98
Other Species Concepts
• Ecological species concept
• Phylogenetic species concept
– Similar ecological niche (what they eat,
how they live, etc.)
– Same species with a unique genetic
history (belong to the same clade; appear
as monophyletic group)
• Good for both sexual and asexual organisms
• Bad for lack of reproductive data and different
species could have similar niche.
• Good for both sexual and asexual, even
fossils; can distinguish sibling species (then
confirmed with BSC)
• Bad for its requirement of extensive
information (time and money as well as man
hours)
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Other Species Concepts
Speciation
• Conclusion:
• Speciation
– Each species concept provides framework
to work with in its respective research
areas.
– The origin of new species.
– There are two ways gene flow between
subpopulations can be interrupted.
• Allopatric speciation
• Sympatric speciation
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102
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Allopatric Speciation
• Allopatric speciation
Two main modes of speciation
– Greek allos=other, patra=homeland
– Gene flow interruption
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Allopatric Speciation
104
Allopatric Speciation
– When subpopulation divided with
geographic barrier (or distance)
– Small populations diverge from large
population
• Barriers’ effectiveness depending on mobility
of organisms (birds vs turtle vs plants).
• Genetic differences accumulate over time
(mutations)
• Allele frequencies altered by selection, drift
• Just 2 million years plants and animals
from S.America evolved to new species
on Galápagos.
• Small populations also proned to
extinction.
105
Harris’s antelope squirrel
(Ammospermophilus harrisi) of
the southern rim of the Grand
Canyon.
106
Can divergence of
allopatric fruit fly
populations lead to
reproductive isolation?
White-tailed antelope squirrel
(Ammospermophilus leucurus)
of the northern rim of the Grand
Canyon.
Starch Population
Starch flies tend to
mate with other starch
flies.
Allopatric speciation of antelope squirrels on opposite rims of the Grand Canyon.
Birds and other organisms that can disperse across the Grand Canyon
have not diverged into different species on opposite rims.
107
The barrier is not
absolute, some
flies mate with
other flies from
different
population.
Maltose Population
Maltose flies
tend to mate
with other
maltose flies.
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18
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Allopatric Speciation
• Allopatric speciation
– Geospiza difficilis
• Females respond to song of same island
males, but ignore songs from other island
males.
– Prezygotic barrier (behavioural isolation)
– Geographic barrier
• Not a reproductive barrier by itself.
– Female’s mate choice (mating song
discrimination)
• A reproductive barrier in this finch species.
19
Sympatric Speciation
Polyploidy
• Sympatric speciation
• Polyploidy
– Greek syn=together, patra=homeland
– Mutation that increase extra set of
chromosomes.
– Rare in animals, but more common in
plants.
• How can reproductive barriers (reduction in
gene flow) between sympatric populations
evolve when members remain in contact?
– Chromosomal mutation
» Polyploidy
– Nonrandom mating
» Habitat differentiation
» Sexual selection
• Autoploidy
– Extra set of chromosome originate from a
single species (Greek: autos=self)
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Polyploidy
• Mechanism
– Nondisjunction in cell division (2n→4n)
• Results
– 2nx4n→3n which is sterile
– 4n can self and mate with other 4n
– In ONE generation, autoploidy generates
isolation without any geographic barrier.
Sympatric speciation by autopolyploidy in plants
117
Sympatric Speciation
118
Sympatric Speciation
• Allopolyploid
• Allopolyploid
– Greek allos=other
– Mechanism
– Result
• When 2 species interbreed and produce sterile
hybrids → this hybrid can asexually reproduce
• Or, with some events, allopolyploid will emerge
(see figure)
119
• Allopolyploid that can interbreed with each
other, but not with its both parent species.
• Allopolyploid plant represents a new biological
species.
• Speciation without geographic barrier.
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20
One mechanism for allopolyploid speciation in plants
121
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Sympatric Speciation
• Polyploid species
– The goatbeard plants
(genus Tragopogon)
• Diploid species
– T. dubius, T. pratensis and T.
porrifolius
• Tetraploid species
– T miscellus (T. dubiusxT.
pratensis)
• Allopolyploid species
http://ftp.funet.fi
123
– T mirus (T. dubiusxT.porrifolius)
– With ongoing hybridization with
its parent species.
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Sympatric Speciation
• Agricultural crops are polyploid
– Oats, cotton, potatoes, tobacco
and wheat
– The bread wheat (Triticum
aestivum)
• Allohexaploid
– Six sets of chromosomes, two
sets from 3 different species
– First polyploid might occur
naturally in the Middle East,
approximately 8,000 years ago.
– Breeding program can be used to
create allopolyploid species.
• Chemical can be used to induce
meiotic and mitotic errors.
http://www.littletree.com.au/bread.htm
125/239
126
21
Sympatric Speciation
• Habitat Differentiation and Sexual
Selection
– The North American apple maggot fly
(Rhagoletis pmonella)
• Reproductive isolation occurs as
subpopulation prefer different food than parent
population (native hawthorn trees).
127
128
Sympatric Speciation
• The lake Victoria
– Only 12,000 years old, but there are 500
species of cichlid fishes. Similar
genetically, suggested that they diverged
just recently, probably from food
preferences.
http://www.pbase.com/crocodile/image/32253695
129
Sympatric Speciation
130
Does sexual selection in cichlids result in
reproductive isolation?
• Pundamilia pundamilia and P. nyererei
Under normal
light, females of
both species mate
with male of the
same species.
– Sexual selection → females select males
from appearance.
– Nonrandom mating, but pollution is
clouding the water.
Under
monochromatic
orange light,
females of both
species mate
indiscriminately
resulting in hybrid
and viable hybrids.
Males and females of Pundamilia pundamilia and P. nyererei
131
Mate choice based on male colouration by females is
reproductive barrier. As prezygotic become breached in the lab it
suggests that genetic different is small and the speciation occur
just recently.
132
22
Adaptive Radiation
• Adaptive radiation
– Evolution of many diverse species
• In new environment with many ecological
niches to occupy.
• Same habitat, but after mass extinction (just
what thought to happen 65 MYA, when
dinosaurs gave way to mammals to diversify.
Seeds
– Hawaii archipelago
– Australia
133
Long-distance dispersal: seeds of Pisonia plant on black
noddy tern and Velcro invention.
134
The Genetic of Speciation
• The monkey flowers (Mimulus lewisii
and M. cardinalis)
Dubautia laxa
Argyroxiphium sandwicense
Dubautia linearis
– Mechanism
• Prezygotic isolation (different pollinators)
• Postzygotic isolation (none; hybrid is viable
and fertile)
– Genetic level
Dubautia waialealae
• Mutations at two loci; one for flower colour,
another for nectar availibility.
Dubautia scabra
Adaptive radiation of the silversword alliance came from only
one species of tarweed about 5 million years ago (molecular
analysis).
135
136
http://www.nsf.gov/od/lpa/news/03/images/mimulus_cardinalis_lewisii.jpg
137
138
http://www.stauder.net/bildearkiv/Mimulus%20lewisii%205.jpg
23
http://visionlab.bio.unc.edu/images/mimulus.image.png
The Tempo of Speciation
• Gradualism
– Descent with gradual modification
(Darwin)
– Little changes accumulate over time.
– Species continuously adapted to the
environment.
• Real evidence or just incomplete data?
– Not all of the changes can be fossilized
(physiological or biochemical changes)
139
140
The Tempo of Speciation
• Punctuated equilibrium
Two models for the tempo of
speciation
– Niles Eldredge and Stephen Jay Gould
– Long stasis, punctuated by sudden
change.
Gradualism model
Punctuated equilibrium model
• Real evidence or just incomplete data?
– Incomplete fossil data set appears to be punctuated.
• Both tempo is possible.
142
141
Macroevolution
Macroevolution
• Macroevolution
– Evolutionary changes above species
levels.
– As small differences accumulated, it would
become clear and more pronounced.
143
• Evolutionary novelties
– Descent with modification
• Complex structure evolved from
something thing with same basic
function.
– How would human eyes have evolved in
gradual increments?
– How would simple eyes be any use to the
ancestors?
» Only complicate eyes are useful?
Certainly not.
144
24
A range of eye complexity among molluscs
Macroevolution
Patch of pigmented cells in limpet (mollusc)
Eyecup in another mollusc
• Evolutionary novelties
– Exaptation
Pinhole camera-type eye (no lens)
in Nautilus (mollusc)
• Structures that evolve for one thing, but
have another function sometime later
(feather and flying).
Eye with primitive lens (transparent
epithelium) in Murex (mollusc)
145
Evolution and Development
Complex camera-type eye in squid
(mollusc), similar to vertebrate eyes,
but evolve independently
146
Evolution and Development
• Genes that control development
• Genes that control development
– How slight genetic divergences can be
magnified into major differences between
species?
• Genes that control development: rate, timing
and spatial patterns; from zygote to adult.
– Allometric growth
• Greek: allos=other + metron=measure
• Different growth rate and pattern during
development alters body proportions.
– Human body and limbs
– Human and chimp skulls
– Salamander feet
– Heterochrony
• Greek: hetero=different + chronos=time
• Change in rate and timing of development
events.
147
148
Different
Time
Allometric growth
Heterochrony
Differential growth rates in human.
Legs and arms lengthen more than
head and trunk.
Comparison of chimpanzee and
human skull growth.
Salamanders that live on
tree have their digit
development end sooner,
giving more webbing to
developed for tree
climbing.
Similar for both chimpanzee and
human in fetus.
In adult, human skull become
rounded with little sloping whereas
chimp skull become elongated wilth
sloping face.
149
Short, but more webbing
150
25
Changes in Spatial Pattern
Different regions of Hox
genes expression in
chicken and fish.
Homeotic genes
Determine where basic
structures (a pair of
wings or legs) will
develop.
Paedomorphosis – retaining larval characteristics even in
adult form (full size, sexually mature).
151
152
Grazers
Hox mutations and the origin of vertebrates
Invertebrate with one copy of
Hox complex
First duplication occurred 520 MYA
New set of genes with new role of
backbone development.
Second duplication 425 MYA yielding 4
set of Hox complexes made jaws and
limbs development possible.
153
Browsers
Yellow line indicates
the evolution of
modern horse with
trend toward
increasing size,
reduced number of
toes and grazing
adaptations.
Evolution is not goal-oriented.
154
Modern Synthesis
• The modern synthesis
– Darwin
Population Genetics
• Quantitative characters (continuous) →
multiple genes with Mendelian inhertitance
– Mendel
The study of allele frequencies
dynamic in a population.
• “Either or” (red or white flower)
– Modern synthesis
• Integrated theory of evolution from Darwin,
Mendel and mathematics.
156
26
Modern Synthesis
Modern Synthesis
• The modern synthesis
• The modern synthesis
– Theodosius Dobzhansky (1900-1975) a geneticist
– R.A. Fisher (1890-1962)
– Ernst Mayr (1904-2005) a biogeographer
– J.B.S. Haldane (1892-1975)
– George Gaylord Simpson (1902-1984) a
paleontologist
– Sewall Wright (1889-1988) a geneticist
– George Ledyard Stebbins (1906-2000) a botanist
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Introduction
• Population genetics
– The study of allele frequency distribution
at the population level.
Sir Ronald Aylmer Fisher
John Burdon Sanderson
Haldane
Sewall Green Wright
– Gene pool
• All the genes present in breeding population at
a given period.
– Allele frequency
George
Ledyard
Stebbins
George Gaylord Simpson
Ernst Mayr
Theodosius Dobzhansky
• Proportion of a given allele to the total allele of
that locus in a population.
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Allele Frequency
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Allele Frequency
• Allele
• Allele frequency (gene frequency)
– Alternate version of a gene at a given
locus on a chromosome.
– For diploid organism, there are two alleles
(A or a) at a locus on homologous
chromosomes.
– Diploid organism
• There are two alleles on the homologous locus
on each chromosome.
• Frequency of allele A is p.
• Frequency of allele a is q.
– There could be more than two alleles as well, called
multiple alleles (i.e. ABO bloodtype; IA, IB and i).
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Total Alleles
Randomly Pick a Gamete
• Total alleles
• Probability
– At a particular time, a total of all genes in
the population is called gene pool.
– Probability of getting gamete containing
allele A is p.
• The total alleles at a locus is 2N in diploid
organism because there are two set of
chromosomes in the nucleus.
– However, in Y-linked genes, there is only 1 Ychromosome per nucleus. Eventhough the organism
is diploid, there is only one copy of Y-linked gene in
the cell.
» The total of alleles on any loci on Y-chormosome
is only N.
– Probability of getting gamete containing
allele a is q.
• The probability of getting either gamete
containing allele (A) or (a) is p+q=1.
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Fertilization of Gametes
Random Zygote
• Zygote
• Fertilization of gametes
– After fertilization of two gametes, one from male
and another from female.
– Zygote = fertilization of 2 gametes.
• Probability of getting one gamete containing
allele (A) and another gamete containing allele
(A) is pxp = p2.
• Probability of getting one gamete containing
allele (a) and another gamete containing allele
(a) is qxq = q2.
• Probability of getting zygote (AA) is pxp = p2.
• Probability of getting zygote (aa) is qxq = q2.
• Proability of getting zygote (Aa) is pxq = pq.
• Proability of getting zygote (aA) is qxp =qp.
• Probability of getting heterozygotes (Aa) or (aA) is pq+qp
= 2pq.
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Total Possible Zygotes
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Allele and Genotype Frequencies
• Total possible zygotes
• Allele frequency
– Homozygous zygotes (AA) or (aa) is p2 or
q2.
– Heterozygous zygotes (Aa) is 2pq.
– p+q = 1
• Genotype frequency
– p2+2pq+q2 = 1
• Probability of getting zygotes (AA) or (aa) or
(Aa) is p2+2pq+q2=1
• Binomial expansion
– (p+q)2 = p2+2pq+q2 = 1
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Polyploidy
Genotypic and Allelic Frequencies
• Haploid
– (p+q)1 = p+q = 1
• Diploid
– (p+q)2 = p2+2pq+q2 = 1
• Triploid
– (p+q)3 = p3+3p2q+3pq2+q3 = 1
• Tetraploid
Heterozygote frequency will be at maximum in a diploid
two-allelic population when allelic frequencies p and q
are equal at 0.5.
– (p+q)4 = p4+4p3q+6p2q2+4pq3+q4 = 1
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Pascal’s Triangle
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Multiple Alleles
• Multiple alleles
n=
– There are more than two alleles at a gene
locus.
0
1
1
11
2
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3
1331
4
14641
5
1 5 10 10 5 1
6
1 6 15 20 15 6 1
7 1 7 21 35 35 21 7 1
8 1 8 28 56 70 56 28 8 1
• Example: ABO bloodtype
– Three alleles IA, IB, and i
– Allele frequencies p, q, and r
– p+q+r = 1
– (p+q+r)2 = p2+q2+r2+2pq+2pr+2qr = 1
– Trinomial expansion
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Obtaining Allele Frequencies
• Techniques for obtaining gene
frequencies
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Numerical Gene Counts
• Numerical gene counts
– There are 400 genes in 200 diploid
individuals.
– Diploid population of 200 individuals
• There are 90 TT, 60Tt and 50tt (200 indv.)
• Using numerical gene counts
• Using genotype frequencies
– T = 180 (TT) + 60 (Tt) = 240/400 = 0.6
– t = 100 (tt) + 60 (Tt) = 160/400 = 0.4
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Using Genotype Frequencies
• Using genotype frequencies
Conclusion
• Two parental populations
– From 90(TT), 60(Tt), and 50(tt) (200 indv.)
– Genotype frequencies
– Genotype frequencies
• TT = 0.45, Tt = 0.30, and tt = 0.25
• TT = 0.40, Tt = 0.40, and tt = 0.20
• 90/200 = 0.45 (TT)
• 60/200 = 0.30 (Tt)
• 50/200 = 0.25 (tt)
• Two offspring populations
– Genotype frequencies
• TT = 0.36, Tt = 0.48, and tt = 0.16
• T = 0.45 (TT) + 1/2(0.30)Tt = 0.45+0.15 = 0.60
• t = 0.25 (TT) + 1/2(0.30)Tt = 0.25+0.15 = 0.40
– Allele frequencies
• T = 0.6 and t = 0.4
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Conclusion
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Conservation of Gene Frequency
• Random mating
• Conservation of gene frequency
– In large populationg with random mating
– After rediscovery of Mendelian genetics
• Genotypic frequencies could be altered by
random mating.
– As can be seen by genotypic frequencies differences
between parental generation vs offspring generation.
• However, random mating does not change
allele frequencies of the population from one
generation to the next.
• Frequency of dominant allele will reach
equilibrium frequency, ratio of 3:1 (3 dominants
to 1 recessive individual).
– Not true for dominant allele that occurs at low
frequency of “brachydactyly” (short fingers).
– Hardy and Weinberg disproved it in 1908.
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The Hardy-Weinberg Theorem
The Hardy-Weinberg Theorem
• Hardy-Weinberg theorem
(1908)
Godfrey Harold Hardy
– Frequencies of alleles and
genotypes remain
constant from generation
to generation.
• Allele frequencies
preservation
Godfrey Harold Hardy
– Genetic variations are
preserved that natural
selection can act over
many generations.
• Not evolving gene pool
• Only Mendelian segregation
and recombination occur.
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Wilhelm Weinberg (1862 — 1937)
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Wilhelm Weinberg (1862 — 1937)
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Hardy and Weinberg
Hardy-Weinberg Equilibrium
• Equilibrium frequencies
• Conservation of gene frequency
– Population that has no change in allele
and genotype frequencies over
generations.
– Gene frequencies do not depend upon
dominance or recessiveness, but remain
essentially unchanged from one
generation to the next under certain
conditions.
• Random mating in large population (no drift)
• No selection, mutation and gene flow.
– Gene frequencies remain constant over generations.
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Equilibrium at Multiple Loci
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Sex Linkage
• Sex-linked genes
• Equilibrium at one locus
– Genes on sex chromosomes (X,Y in
human)
– Only one generation is needed for the
population to reach equilibrium.
• Equilibrium at multiple loci
• There are 5 genotypes for X-linked genes, for
allele A and a on gene locus A.
– If genes are linked and not segregated
independently, equilibrium cannot be
reached in one generation.
– In female: AA, Aa, and aa (two X chromosomes).
– In male: A and a (only one X chromosome;
hemizygous)
» Allele frequencies are the same in both sexes,
whereas genotype frequencies are different.
• Given more time, it could reach equilibrium.
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Equilibrium in Natural Populations
• How to study equilibrium in real
populations?
– This can be done if all segregants can be
scored.
• Observed phenotypes reflect genotypes.
– Codominant alleles
» MN blood group
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American Ute Indians
American Ute Indians
• Is this population at HWE?
• MN blood groups
– Phenotype/genotype frequencies
– Population size, n, 104 individuals
– Phenotype/genotype frequencies
• 0.59 MM, 0.34 MN, 0.07 NN
– Observed allele frequencies
• 0.59 MM, 0.34 MN, 0.07 NN
• M = 0.59 + (0.34/2) = 0.76
• N = 0.07 + (0.34/2) = 0.24
– Allele frequencies
• M = 0.59 + (0.34/2) = 0.76
• N = 0.07 + (0.34/2) = 0.24
– Calculated allele frequencies
• MM = (0.76)2 = 0.58
• MN = 2(0.76)(0.24) = 0.36
• NN = (0.24)2 = 0.06
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Albinism
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HWE at Multiple Loci
• Albinism
• HWE at multiple loci
– Albinism affects 1 in 20,000 individuals.
– HWE can also be studied, for example of
three alleles system: p, q, and r.
• q2 = 1/20,000 = 0.00005
• q = 0.007
2( A1A1) + ( A1A2) + ( A1A3)
2N
2( A2 A2) + ( A1A2) + ( A2 A3)
q=
2N
2( A3 A3) + ( A1A3) + ( A2 A3)
r=
2N
p=
• p = 1-q
• p = 0.993
• Heterozygotes (carriers) = 2pq = 0.014
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Inbreeding
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Factors Affecting Allele Frequencies
• Inbreeding
• Population can deviate from HWE
– Related individuals of similar genotype mated
preferentially with each other.
• Selfing (self breeding, self fertilization)
– Two gametes from a single individual fertilized to
form zygote.
• Consequences
– Mutation
– Selection
– Migration
– Random genetic drift (small population
size)
– Not alter allele frequencies.
– But inbreeding will lead to excess of
homozygotes.
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Mutation
Mutation
• Mutation
• Mutation
– Changes in the nucleotide sequence of
DNA.
– Difficult to predict what mutation will
bring.
– Mutation in somatic will be lost, only in
germ cell line will be passed on to next
generation.
• Point mutation
– Change only one base.
– Most of the point mutation has little to no effect.
• Mutation rate is low in animals and plants (1
mutation in 100,000 genes per generation)
• Gene duplication
– Increase gene number (1000 olfactory genes in
human (60% inactive), 1300 in mice (20% inactive))
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Diverse colour pattern of these mustangs are the product of past mutations.196
Mutation
• Mutation
• Chromosomal mutations
–Deletion, insertion, inversion,
translocation (change expression
level)
Recombination
Recombination
• Recombination
• Sexual reproduction
– Interchromosomal recombination
– Rearrange alleles into fresh combinations
every generations.
• Independent assortment
• Sexual reproduced organisms lack
recombination, has little genetic variations.
– Intrachromosomal recombination
• Crossing over
– No new genetic variations
– Reshuffling existing genetic variations
• Bacteria and virus also have different version
of recombination, plus their high mutation
make them very dangerous.
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Natural Selection
Natural Selection
• Natural selection
• On HWE
– Better individuals (fitter; better surviving
and reproduction) will leave more
offspring than less fit.
– Differences in survial and reproductive
success would disturb HWE.
• Red flowers (CRCR)
– would produce more offspring (set more
seeds) as they attract more pollinators.
» Frequency of CR would increase whereas
CW decline.
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Genetic Drift
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Genetic Drift
• Genetic drift
• The bottleneck effect
– Fluctuation of allele frequency from
generation to generation.
– Drift tend to reduce genetic variation, lead
to fixation of genes.
– A population is forced through a
restrictive “bottleneck” such as
disasters (storm, flood, drought).
• Gene pool of this surviving population
would be different from the original.
– Small population is the most affected by
drift.
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Genetic Drift
• The founder effect
– A small population (or even one fertilised
female) becomes isolated from its large
population, and establish new population,
possibly in the new location.
• Isolation bottleneck
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Gene Flow
• Gene flow
– Movement of the gene from one population
to another.
• Movement of individuals for animals, or plants’
seeds
• Movement of gametes for plants as in pollen
via pollinators
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Gene Flow
• On HWE,
– Immigration and emigration would
increase or decrease allele frequencies in
populations.
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Adaptive Evolution
• Adaptation
– Something that increase fitness of the organisms,
compared to those that don’t.
• Adaptive evolution
– Evolution that occurs to increase fitness of the
organisms.
• Adaptive traits
• Maladaptive traits
• Natural selection
– Only natural selection can lead to adaptation.
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Genetic Variation
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Genetic Variation
• Genetic Variation
• Genetic Variation
– Variation within a population
– Variation between populations
• Polymorphism (as oppose to monomorphic)
• Geographic variation
– More than one morph can be detected (>0.01)
» Phenotypic polymorphism
» Genetic polymorphism
– Cline = a graded change in trait along a geograhpic
axis.
• Measuring genetic variation
– Average heterozygosity (e.g. it is 14% in Drosophila)
» Of all its 13,000 loci → 1,800 loci are
heterozygous.
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Geographic variation in
chromosomal mutations
Fusion of chromosomes (2.4 is between chromosome 2 and
chromosome 4)
Nonheritable variation within a population
European map butterflies (Araschnia levana)
have 2 seasonal forms. If one of these form
have better fitness, there would be no change
in colouration alleles as they are identical
genetically.
This fusion appear to be neutral.
These two patterns (yellow vs red dots) are different.
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cline
Does geographic variation in yarrow plants (Achillea) have a genetic component?
Collecting seeds to grow in the common garden
(same elevation). Plants’ height reflect both genetic
variation and environmental effects.
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Fitness
Fitness
• Fitness
• Fitness
– How well the organism survive and
reproduce.
• Inclusive fitness
– Inclusive fitness = direct fitness + indirect fitness
• The contribution an individual makes to the
pool of the next generation, relative to the
constribution of other individuals.
– Relative fitness
• The contribution of a genotype to the next
generation compared to the contributions of
alternative genotypes for the same locus.
– Range from 1 to 0.
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Mode of Selection
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Mode of Selection
• Disruptive selection
• Mode of selection
– Selection that favour extreme traits, but
against intermediate traits. This mode could
lead to speciation. (finch’s beak)
– Natural selection can alter
phenotypic distribution in 3 ways.
• Stabilizing selection
• Directional selection
– Selection that favours intermediate traits,
but against extreme traits. This mode
reduces variation. (human birth weight)
– Selection that deviate from average to one
of the directions. (fossil bears)
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The Preservation of Genetic Variation
The Preservation of Genetic Variation
• Why recessive alleles remain in the
population?
• Why recessive alleles remain in the
population?
– Diplody
– Neutral variation
• Dominant alleles conceal recessive alleles in
heterozygote.
• Neutral mutations, pseudogenes → no effect
on fitness
– Balancing selection (balanced
polymorphism)
– Sexual selection
• Heterozygote advantage (malaria-sickle-cell
anemia)
• Frequency-dependent selection (the rarer, the
better)
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• Selection for showy trait (reduce fitness of
male), but could reflect that the showy male
has better genes.
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Frequency-Dependent Selection
• Frequency-dependent selection
– Fitness of the organism depending on its
own frequency.
• Example
– Predator-pray relationship
» Batesian mimicry
» Search images
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Phenotypic
variation
Generation time
Frequency
independent
selection
Using a virtual population to study the
effects of selection
Blue jay recieves a food reward it
can peck a screen with virtual moths.
Patterned digital moths are harder to
detect
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Evolution of Sex
Evolution of Sex
• Evolution of sex
• Evolution of sex
– How did sex evolve in the first place?
– To increase population expansion?
(asexual is better)
• Reproductive handicap of sex
– Majority of eukaryotes reproduce
sexually.
– What advantage does sex provide?
• Despite sex’s reproductive drawback,
sexual reproduction is favoured by
natural selection because sex generates
genetic variations enable future
adaptation to ever-changing
environment.
– Asexual population increase rapidly
compared to sexual population (assuming
that 2 surviving offspring per female).
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Evolution of Sex
• Evolution of sex
• Coevolution between species and
its pathogen
–(Red Queen race: Alice to run as fast
as she could just to stay in the same
place)
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Sexual dimorhism and sexual selecion in peacocks and peahens.
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Perfect Oranism
• Why could natural selection not create
“perfect organism”?
– Evolution is limited by historical
constraints.
– Adaptations are often compromises.
– Chance and natural selection interact.
– Selection can only edit existing variations.
The reproductive handicap of sex
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Perfect Oranism
References
• Better than…
• Textbooks
– Natural selection can select better trait,
compared to other
– Campbell, N. A. (2008). Biology. San
Francisco, Pearson Benjamin Cummings.
– Starr, C. (2006), Basic Concepts in Biology
(the 6th edition). Thomson Brooks/Cole.
USA.
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