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Unit 3: Evolution
Chapter 19: Descent with modification
What lead
Darwin to his
idea of
evolution?

In The Origin of Species Darwin proposed that Earth’s many species are
descendants of ancestral species that were different from the present-day species
...
Evolution can be
viewed in two related but different ways: as a pattern and as a process
...
The process of evolution
consists of the mechanisms that produce the observed pattern of change
...

Scala Naturae and Classification of Species
 Aristotle viewed species as fixed, recognized certain “affinities”
among organisms  believed life forms could be arranged on a ladder of
increasing complexity called Scala Naturae (the scale of Nature)
...

 Old ideas were consistent with Old Testament belief that species
were individually designed by god/ perfect & in the 1700s many scientists
interpreted an organism’s match to their environment as evidence that God had
designed each species for a particular purpose
...
New layers of sediment cover older ones
and compress them into layers of rock called strata
...

 Observed that from one layer to the next, some new species appeared while
other disappeared
...
He reasoned that such regions were later
populated by different species, emigrating from other areas
...
 1795,
Scottish geologist James Hutton  proposed that Earth’s geologic features
could be explained by gradual mechanisms (valleys being formed by rivers
wearing through rocks)  Charles Lyell, leading geologist of Darwin’s time,

proposed that the same geological processes are operating today as in the past
and at the same rate
...
He later figured that similar slow and subtle processes could
produce substantial biological change
...
 explained his findings with two principles: 1
...
2
...
Henslow recommended him to Capt
...

The Voyage of the Beagle
 Left on December 1831
...
– Darwin spent most of his time
on shore, observing and collecting thousands of plants and animals – noted that
the characteristics that made organisms well suited to their environments 
 Observed that plants and animals in more temperate regions of
South America, closely resembled species living in temperate regions of
Europe
...
 Darwin
hypothesized that the Galapagos had been colonized by organisms that had
strayed from South America and then diversified, giving rise to new species on
the various islands 
Darwin’s Focus on Adaption
 Adaption: inherited characteristics of organisms that enhance their
survival and reproduction in specific environments – reassessed his
observations, began to perceive adaption to the environment and the origin of
new species as closely related processes  biologists concluded that new

What
evidence
proves
evolution?

species arise from gradual accumulation of adaptions to a different environment
 the finches’ various beaks and behaviors are adapted to the specific food
available on their home islands
...

 In the 1840s, Darwin was working on putting his hypothesis into a
paper but was reluctant to published due to the anticipated uproar  continued
to compile evidence – by mid 1850s Darwin described his hypothesis to Lyell
and a few other and even though Lyell wasn’t a believer, he urged Darwin to
publish before someone else came to similar conclusions and published before
him 
 Lyell was right – Alfred Russell Wallace sent a manuscript to Darwin
for review in June 1858 and he developed a hypothesis of natural selection
nearly identical to Darwin’s
...
had convinced most scientists that evolution caused life’s diversity
Ideas from The Origin of Species
 Darwin gathered evidence that descent with modification by natural selection
explain three broad observations: the unity of life, the diversity of life, and the match
between organisms and their environments 
Descent with Modification
 descent with modification = evolution
 Beak length evolution experiment  Soapberry Bug populations that
feed on plants introduced to Louisiana, Oklahoma, and Austrailia
...
Thus, in populations feeding on introduced species in these
regions, the researchers predicted that natural selection would result in the
evolution of longer beaks
...

 natural selection can cause rapid evolution in a wild population
The Evolution of Drug-Resistant Bacteria
 Example of Ongoing natural selection: the evolution of drug-resistant
pathogens (disease causing organisms and viruses)
...
aureas (MRSA) – in the past decade there has been an alarming increase in
virulent forms of MRSA such as clone USA300, a strain that can cause flesh
eating disease 
 In 1943, penicillin became the first widely used antibiotic – although it
saved many lives by 1945 over 20% of MRSA strains seen in hospitals were
resistant to penicillin – these strains had an enzyme that could destroy penicillin
called penicillinase  researchers developed antiboditics that were not
destroyed by penicillinase, but some strains developed resistance to each new
drug within a few years
...


 natural selection is a process of editing, not creative mechanism  a
drug does not create a resistant pathogen, it selects for resistant individuals that
are already present in the population  natural selection depends on time and
place – it favors those characteristics in a generally variable population that
provide advantage in the current local environment – what is beneficial in one
situation may be useless or even harmful in another 
Homology
 type of evidence for evolution comes from analyzing similarities
among different organisms  Characteristics present in an ancestral organism
are altered by natural selection in its descendants over time as they face different
environmental conditions  related species can have characteristics that have
an underlying similarity yet function differently
...
Some of these shared
features only make sense in context of evolution  Example: limbs of all
mammals show the same arrangement of bones from the shoulders to the tips
of the digits, even though these appendages have very different functions 
The skeletons of the arms, forelegs, flippers, and wings of different mammals
are homologous structures that represent variations on a structural theme that
was present in their common ancestor
...
 Ex: At some point all
embryos have a tail (behind the anus) and pharyngeal (throat) arches
...
 Ex: skeletons of some snakes retain
vestiges of the pelvis and leg bones of walking ancestors – eye remnants buried
under the scales in blind species of cave fish
...
 it is common for organisms to have genes in
related species may be fully functional
...

A Different Cause of Resemblance: Convergent Evolution
 distantly related organisms can resemble one another because of
convergent evolution: the independent evolution of similar features in different
lineages  Ex: Sugar Gliders (Australia) and Flying Squirrels (North America)
 although they evolved independently from different ancestors, these two
mammals have adapted to similar environments in similar ways  Analogous:
features among species shared due to convergent evolution/ features that share
similar functions, but not similar ancestry 
The Fossil Record
 fossils documents the patterns of evolution showing that past
organisms differed from present day organisms and that many species have
become extinct  fossils show the evolutionary changes that have occurred in
various groups of organisms  fossils can shed light on the origins of new
groups of organisms 

 The fossil record shows that over time, descent with modification
produced increasingly large differences among related groups of organism
...
250 million years ago  was Pangaea  can use our understanding
of evolution and continental drift to predict where fossils of different groups of
organisms might be found 
 Can use our understanding of evolution to explain biographic data 
Example: islands that have many plant and animal species are endemic (they are
nowhere else in the world)  most island species are closely related to species
from the nearest mainland or a neighboring island – Darwin explained this
observation by suggesting that islands are colonized by species from the nearest
mainland – these colonists eventually gave rise to new species as they adapt to
their environments 
What is theoretical about Darwin’s view of life?
 Pattern of evolution: the observation that life has evolved over time  has
been documented directly and is supported by a great deal of evidence
...
B 2
...
D 4
...
A 6
...

systematics: a discipline focused on classifying organisms and determining their
evolutionary relationships
...
1: Phylogenies show evolutionary relationships
 Taxonomy: how organisms are named and classified
Binomial Nomenclature
 Binomial instituted by Carolus Linneaus – two part naming system --first part is the name of the genus --- second part is the specific epithet (Pathera
pardus)  *take note that the first letter of the genus is capitalized and the rest
of the letters are italicized 
Hierarchical Classification
 species grouped into increasingly inclusive categories  (Inclusive to
Broad) Species  Genus  Family  Order  Class  Phylum  Kingdom
 Domain
 Ex: Leopard Panthera pardus  Panthera  Felidae  Carnivora
 Mammalia  Chordata  Animalia  Eurkarya
 Linnaean system: the taxonomic system  Taxon: (pl
...
, do not necessarily
reflect evolutionary history  reasons why this may happen: 1
...
2
...
 Sometimes a species is placed within a
genus to which it is not most closely related
...
 these relationships are often depicted as two way branch points

 Sister taxa: groups of organism that share an immediate ancestor/ closest

relatives  Basal taxon: a lineage that diverges early in the history of a group 
Polytomy: a branch point from which more than two descendant groups emerge
 signifies that evolutionary relationships among the taxa are not clear yet 
What We Can and Cannot Learn from Phylogenic Trees
Applying Phylogenies
1
...
Although closely related organisms often resemble one another, they
may not if their lineages have evolved at different rates or faced very
different environmental conditions
3
...
We should not assume that a taxon on a phylogenetic tree evolved
from the taxon next to it
...
2: Phylogenies are inferred from morphological and molecular data
To infer phylogeny, systematists must gather as much information as possible
about the morphology, genes and biochemistry of the relevant organisms
...

Morphological and Molecular Homologies
 Homologies: phenotypic and genetic similarities due to shared
ancestry (skeletal structure, DNA, genes)  organisms that share similar
morphologies or similar DNA sequences are likely to be more closely related
than organisms with vastly different structures or sequences
...

 Essential to distinguish between homology and analogy in
reconstructing phylogenies  Homoplasies: analogous structures that arose
independently  another clue to distinguishing between homology and analogy
is the complexity of the character being compared  the more elements that
are similar in two complex structures, the more likely it is that they evolved
from a common ancestor  Same argument applies to comparison of genes, if
genes in two organisms share many portions of their nucleotide sequences, it is
likely that the genes are homologous
...
If the species are very
closely related, the sequences form the species probably differ at only one or a
few sites
...

 Researchers have developed computer programs that estimate the best
way to align comparable DNA segments of differing lengths 
How are
shared
characters
organized on
phylogenic
trees?

20
...

Polyphyletic: group that includes taxa with different ancestors
...
 Outgroup: a species or group of
species from an evolutionary lineage that is known to have diverged
before the lineage that includes the species being studied
...
 Even though the branches of a phylogenetic
tree may have different lengths, among organisms alive today, all the different
lineages that descend from a common ancestor have survived for the same
number of years
...
 These equal
spans of chronological time can be represented in a phylogenetic tree whose
branch lengths are proportional to time
...
 it is possible to
combine these two types of tress by labeling branch points with information
about rates of genetic change or dates of divergence
...
 Scientists have
developed many computer programs to search for organisms that are
parsimonious
...

Phylogenetic Bracketing: using this approach we can predict that features shared
by two groups of closely related organisms are present in their common
ancestor and all of its descendants unless independent data indicates otherwise
...
4: Molecular clocks help track evolutionary time
 Evolutionary biology strives to understand the relationships among all
organisms (including those without a fossil record) and to attempt to determine the
timing of phylogenies they rely on an assumption about how change occurs at the
molecular level
...
– An assumption
underlying the molecular clock is that the number of nucleotides substitutions
in related genes is proportional to the time that has elapsed since the genes
branched from their common ancestor
...
rate of
evolution is calibrated against the dates of evolutionary branch points from the
fossil record
...

Differences in Clock Speed
 some mutations may be selectively neutral (neither beneficial
or detrimental)  if most of the mutations are selectively neutral then
the rate of evolution for these mutations should be regular 

like genes
evolve?

differences in the clock rate for different genes are a function of how
important a gene is – if the exact sequence of amino acids that a gene
specifies is essential to survival, most of the mutations will be harmful
and only a few will be neutral  these genes change slowly  If the
exact sequence of amino acids is less critical, fewer of the new
mutations will be harmful and more will be neutral  genes change
more quickly 
Applying a Molecular Clock: Dating the Origin of HIV
 researchers have used a molecular clock to date the origins of HIV
infections in humans  Phylogenetic analysis shows that is descended from
viruses that infect chimpanzees and other primates (most of these viruses do not
have AIDS-like diseases in their native hosts
...


Why is
horizontal
gene transfer
important?

20
...

The important Role of Horizontal Gene Transfer
 Phylogenies based on rRNA genes suggest that eukaryotes are most closely
related to archaea, while data from some toher genes suggest a closer relationship to
bacteria
...
 Genetic
analyses indicate that extensive horizontal gene transfer has occurred throughout the
evolutionary history 

Chapter 21: The Evolution of Populations
 Natural selection acts on individuals, but the evolutionary impact of natural
selection is only apparent in the changes in a population of organisms over time
...
1 Genetic Variation makes Evolution possible
Genetic Variation
 genetic variation: differences among individuals in the composition of
their genes or other DNA genes  some heritable phenotypic differences
occur on an “either – or” basis  variation usually results from the influence of
two or more genes on a single phenotypic character, many phenotypic
characters are influenced by multiple genes  Characters (like color) that vary
in this way are typically determined by a single gene locus, with different alleles
producing distinct phenotypes  introns: noncoding segments of DNA –
exons: the regions retained in mRNA after RNA processing  some heritable
variation is not heritable  Much of genetic variation can be measured at the
molecular level of DNA nucleotide variability, but little of this variation results
in phenotypic variation because many of the inferences occur in introns 
most of the variations that occur in exons do not cause a change in the amino
acid sequence of the protein encoded by the gene 
Sources of Genetic Variation
 Evolution depends on genetic variation – genetic variation is caused
when mutation, gene duplication, or other processes produce new alleles and
new genes  genetic variants can be produced in short periods of time in
organisms that reproduce rapidly  loci: the place along the length of a
chromosome where a given gene is located 
Formation of New Alleles
 Mutation: c change in the nucleotide sequence of an
organism’s DNA  Only mutations in cell lines that produce gametes
can be passed to offspring in multicellular organisms  in most
animals, the majority of mutations occur in some somatic cells and are
lost when the individual dies  Point Mutation: a change in one base
of a gene  can have significant impact on phenotype  organisms
reflect many past generations of past selection, and hence their
phenotypes tend to be well matched to their environments  it’s
unlikely that a new mutation that alters a phenotype will improve it
...
The result is an expanded genome
with new genes that may take on new functions
...
Results from the unique combination of alleles that
each individual receives from its parents
...

What is the
HardyWeinburg
equation?
How did they
come up with
the HardyWeinburg
equation?

21
...

The Hardy-Weinburg Principle
Hardy-Weinburg Equilibrium
 Hardy – Weinburg Principle: named for British
mathematican and German physican 1908 – states that the frequencies
of alleles and genotypes in a population will remain constant from
generation to generation, provided that only medelian segregation and
recombination of alleles are at work  To use the HWP, view
reproduction as a process of randomly selecting and combining alleles
from a bin (the gene pool), this assumes that mating occurs at random
...

q = recessive allele freq
...
of homozygous dominant
q^2 = heterozygous genotypic freq
...
No Mutations: the gene pool is modified if mutations alter
alleles or if entire genes are deleted or duplicated
...
Random Mating: if individuals tend to mate within a subset of
the population such as their near neighbors or close relatives
(inbreeding), random mixing of gametes does not occur, and
genotype frequencies change
3
...
Extremely large population size: the smaller the population,
the more likely it is the allele frequencies will fluctuate by
chance from one generation to the next (genetic drift)
5
...
3 Natural Selection, genetic drift, and gene flow can alter allele frequencies in a
population
 Violation of any of the HWE condition could result in evolution  Violation
of Condition 1  new mutations can alter allele frequencies, but because mutations are
rare, the change from one generation to the next is likely to be very small
...
Effects of
genetic drift are most pronounced in small populations
...

The Bottleneck effect
 Bottleneck Effect: Genetic drift that occurs when the size of a
population is reduced, as by natural disaster or human actions
...
 If a population that had passed through a bottleneck and
recovers in size, it may have low levels of genetic variation for a long
period of time 
Case Study: Impact of Genetic Drift on the Greater Prairie Chicken
 Greater Prairie Chickens went through a bottleneck of being
converted from prairies to farmland cause the number of Greater Prairie
Chickens plummeted  genetic drift during the bottleneck led to a loss of
genetic variation and an increase in the frequency of harmful alleles 
Effects of genetic Drift: A Summary
1
...
Genetic drift can cause allele frequencies to change at random
Because of GD an allele may increase in frequency one year,
then decrease the next, the change from year to year is not predictable
causes allele frequencies to change at random over time
3
...
Genetic drift can cause harmful alleles to become fixed
Alleles that are neither harmful nor beneficial can be lost or
become fixed entirely by chance through genetic variation
...
 if gene flow in extensive
enough it can result in two populations combining into a single population with
a common gene pool  alleles transferred by gene flow can also affect how
well populations are adapted to local environmental conditions  gene flow
can also transfer alleles that improve the ability of populations to adapt to local
conditions 
21
...

Relative Fitness
 Relative fitness: the contribution an individual makes to the
gene pool of the next generation, relative to the contribution of other
individuals in the population
...
 Disruptive selection: Natural
selection in which individuals on both extremes of a phenotypic range
survive or reproduce more successfully than do individuals with
intermediate phenotypes
...


The Key Role of Natural Selection in Adaptive Evolution
Sexual Selection
 sexual selection: a form of natural selection in which individuals with
certain inherited characteristics are more likely than other individuals to obtain
mates sexual dimorphism: a difference in secondary sexual characteristics
between males and females of the same species  intrasexual selection:
selection within the same sex, individuals of one sex compete directly for mates
of the opposite sex – usually occurs among males  intersexual selection:
individuals of one sex (usually females) are picky in selecting their mates from
the other sex – in many cases the female’s choice depends on the showiness of
the male’s appearance or behavior
...

Recessive alleles that are less favorable than their dominant variation is
exposed to natural selection only when both parents carry the same
recessive allele and two copies end up in the same zygote
...
Heterozygote protection maint
Balancing Section
 Balancing selection: natural selection that maintains two or
more phenotypic forms in a population
...

Frequency- Dependent Selection
 Frequency –dependent selection: selection in which the fitness of a
phenotype depends on how common the phenotype is in a population
...
Selection can act only on existing variations
Natural selection only favors the fittest phenotypes among those
currently in the population, which may not be the ideal traits
...
Evolution is limited by historical constraints
Each species has a legacy of descent with modification from
ancestral forms –evolution co-opts existing structures and adapts them
to new situations / evolution works on existing traits -

3
...


4
...
Ex: population of sparrows flying and some go into/ are
trapped in a garage, while the rest are caught in a storm and die
...

 With these constraints, evolutions does not craft “perfect” organisms
 Natural selection operates on a “better than” basis



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