DNA is the genetic material. The

1
Basic genetics terminology
DNA is the genetic material. The instructions for
making and operating an organism are written in
DNA. DNA is divided into sections called genes.

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What a gene does

• Each gene codes for a single protein. The gene
  specifies the sequence of amino acids that should
  be joined together to make a protein.
• Together the genes determine the characteristics
  of an organism.

3
Alleles and genes

• Alleles are different versions of a
• gene.
• If a single gene codes for flower color, white
  and blue flowers would be coded for by 2
  different alleles.

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Number of copies of genes

• You possess two copies of each gene in
• your body.
• One copy is inherited from each parent.
• For a given gene you may have two
• different alleles or two copies of the same
  allele.
• ( excluding genes on sex chromosomes
• in males).

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Homozygous vs heterozygous

• A homozygous individual has two copies of a
  particular allele. (AA)
• A heterozygous individual has two different
  alleles. (Aa)

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Genotype and phenotype

• An organisms genes (its genotype) play a large
  role in determining its physical appearance (its
  phenotype).
• But remember an organisms phenotype is also
  affected by the environment.

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The relationship between genes and evolution

• We express evolutionary ideas in terms of genes
  because genes are the only thing that are passed
  from one generation to the next.

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Process of Natural Selection

• In the process of natural selection, genes
• that help organisms to survive and reproduce
  become more common.
• Genes that help less or are harmful
• gradually are eliminated from the population.

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Process of Natural Selection

• Individuals that are the best adapted to their
  environments (the best camouflaged, best at
  finding food, etc.) will generally be more
  successful at breeding than less well adapted
  individuals.
• As a result, their genes (which make them well
  adapted) will be commoner in the next generation
  than the genes of less well adapted individuals.

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Chapter 23. The Evolution of Populations

• Remember individual organisms do not evolve.
  Individuals are selected, but it is populations
  that evolve.
• Because evolution occurs when gene pools change
  from one generation to the next, understanding
  evolution require us to understand population
  genetics.

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Some terminology

• Population All the members of one species living
  in single area.
• Gene pool the collection of genes in a
  population. It includes all the alleles of all
  genes in the population.

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Some terminology

• If all individuals in a population all have the
  same allele for a particular gene that allele is
  said to be fixed in the population.
• If there are 2 or more alleles for a given gene
  in the population then individuals may be either
  homozygous or heterozygous (i.e. have two copies
  of one allele or have two different alleles)

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Detecting evolution in nature

• Evolution is defined as changes in the structure
  of gene pools from one generation to the next.
• How can we tell if the gene pool changes from one
  generation to the next?
• We can make use of a simple calculation called
  the Hardy-Weinberg Equilibrium

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Hardy-Weinberg Equilibrium

• Before discussing Hardy-Weinberg need to review
  some basic facts about Mendelian Inheritance.
• In Mendelian Inheritance alleles are shuffled
  each generation into new bodies in a way similar
  to which cards are shuffled into hands in
  different rounds of a card game.
• The process of Mendelian Inheritance preserves
  genetic diversity from one generation to the
  next. A recessive allele may not be visible
  because it is hidden by the presence of a
  dominant allele, but it is still present.

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Hardy-Weinberg Equilibrium

• The shuffling process occurs because an
  individual has two copies of any given gene (one
  inherited from father and one from mother), but
  can put only one or the other copy into a
  particular sperm or egg. E.g. for an individual
  who is heterozygous Aa 50 of sperm will contain
  A and 50 will contain a.

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Hardy-Weinberg Equilibrium

• Individuals alleles thus go through a process
  where they are sorted into gametes (sperm or egg)
  which combine to form a zygote which will one day
  again sort alleles into gametes.
• See Chapter 14 to review Mendelian Inheritance

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Hardy-Weinberg Equilibrium

• Consider a population of 100 individuals. This
  population will contain 200 copies of any given
  gene because each individual has two copies.
• Gene we are interested in has two alleles A and a.

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Hardy-Weinberg Equilibrium

• If 80 of the alleles in the gene pool are A and
  20 are a, we can predict the genotypes in the
  next generation.
• Basic probability To determine the probability
  of two independent events both occurring, you
  should multiply the probabilities of the
  individual events together.

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Hardy-Weinberg Equilibrium

• Probability of an AA individual is 0.80.8 0.64
• Probability of an aa individual is 0.20.2 0.04
• Probability of an Aa individuals is 0.20.8
  0.16, but there are two ways to produce an Aa
  individual so 0.162 0.32.
• Note these probabilities sum to 1.

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Hardy-Weinberg Equilibrium

• General formula for Hardy-Weinberg is
• p2 2pq q2 1, where p is frequency of allele
  1 and q is frequency of allele 2.
• p q 1.

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Hardy-Weinberg Equilibrium

• Hardy-Weinberg equilibrium can be used to
  estimate allele frequencies from information
  about phenotypes and genotypes.

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Hardy-Weinberg Equilibrium

• E.g. approx 1 in 10,000 babies are born with
  phenylketonuria (PKU) (causes retardation if diet
  is not kept free of amino acid phenylalanine).
• Disease due to individual being homozygous for a
  recessive allele k. i.e., the babies genotype is
  kk.

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Hardy-Weinberg Equilibrium

• What is frequency of k allele in population?
• q2 frequency of PKU in population 0.0001.
• q square root of q2 or 0.01. Frequency of
  allele k
• Therefore p the frequency of the K allele 1 -
  0.01 0.99
• Frequency of carriers (heterozygotes) in
  population is 2pq
• 20.990.01 0.0198 or almost 2 of population.
  Much greater than frequency of PKU.

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Working with the H-W equation

• You need to be able to work with the
  Hardy-Weinberg equation.
• For example, if 9 of 100 individuals in a
  population suffer from a homozygous recessive
  disorder can you calculate the frequency of the
  disease-causing allele? Can you calculate how
  many heterozygotes are in the population?

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Working with the H-W equation

• p2 2pq q2 1. The terms in the equation
  represent the frequencies of individual
  genotypes. A genotype is possessed by an
  individual organism so there are two alleles
  present in each case.
• P and q are allele frequencies. Allele
  frequencies are estimates of how common alleles
  are in the whole population.
• It is vital that you understand the difference
  between allele and genotye frequencies.

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Working with the H-W equation

• 9 of 100 (frequency 0.09) of individuals are
  homozygous for the recessive allele. What term in
  the H-W equation is that equal to?

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Working with the H-W equation

• Its q2.
• If q2 0.09, whats q? Get square root of q2,
  which is 0.3, which is the frequency of the
  allele a.
• If q0.3 then p0.7. Now plug p and q into
  equation to calculate frequencies of other
  genotypes.

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Working with the H-W equation

• p2 (0.7)(0.7) 0.49 -- frequency of AA
• 2pq 2 (0.3)(0.7) 0.42 frequency of Aa.
• To calculate the actual number of heterozygotes
  simply multiply 0.42 by the population size
  (0.42)(100) 42.

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Other examples of working with HW equilibrium is
a population in HW equilibrium?

• In a population there are 100 birds with the
  following genotypes
• 44 AA
• 32 Aa
• 24 aa
• How would you demonstrate that this population is
  not in Hardy Weinberg equilibrium

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Three steps

• Step 1 Calculate the allele frequencies.
• Step 2 Calculate expected numbers of each
  genotype (i.e. figure out how many homozygotes
  and heterozygotes you would expect.)
• Step 3 Compare your expected and observed data.
  

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Step 1 allele frequencies

• Step 1. How many A alleles are there in total?
• 44 AA individuals 88 A alleles (because each
  individual has two copies of the A allele)
• 32 Aa individuals 32 A alleles (each
  individual one A allele)
• Total A alleles is 8832 120.

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Step 1 allele frequencies

• Total number of a alleles is similarly
  calculated as 224 32 80
• What are allele frequencies?
• Total number of alleles in population is 120
  80 200 (or you could calculate it by
  multiplying the number of individuals in the
  population by two 1002 200)

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Step 1 allele frequencies

• Allele frequencies are
• A 120/200 0.6. Let p 0.6
• a 80/200 0.4. Let q 0.4

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Step 2 Calculate expected number of each genotype

• Use the Hardy_Weinberg equation
• p2 2pq q2 1 to calculate what expected
  genotypes we should have given these observed
  frequencies of A and a
• Expected frequency of AA p2 0.6 0.6 0.36
• Expected frequency of aa q2 0.40 .4 0.16
  
• Expected frequency of Aa 2pq 2.6.4 0.48

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Step 2 Calculate expected number of each genotype

• Convert genotype frequencies to actual numbers by
  multiplying by population size of 100
• AA 0.36100 36
• aa 0.16100 16
• Aa 0.48100 48

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Step 3 Compare Observed and Expected values

• Observed population is
• 44 AA 32 Aa 24 aa
• Expected population is
• 36AA 48Aa 16aa
• These numbers are not the same so the population
  is not in Hardy-Weinberg equilibrium. An
  assumption of the Hardy Weinberg equilibrium is
  being violated. What are those assumptions?

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Hardy-Weinberg Equilibrium

• Remember that the Hardy-Weinberg equation tells
  us what we would expect to find if alleles are
  simply randomly assorted into gametes and gametes
  come together randomly to produce new genotypes.
• If a population is found to depart significantly
  from H-W equilibrium this is strong evidence that
  evolution is taking place, i.e., the gene pool of
  the population is changing.

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Hardy-Weinberg Equilibrium

• Five Conditions under which Hardy-Weinberg
  equilibrium holds
• No gene flow no migration.
• Random mating no inbreeding.
• No mutations.
• Large population size reduces effects of chance
  events
• No natural selection.

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Gene flow

• Movement of individuals between populations can
  alter gene frequencies in both populations.
• Frequent migration may cause populations gene
  pools to become more similar to each other.

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Non-random mating

• Mating preferentially with others that are
  phenotypically similar to you in extreme cases
  inbreeding (mating with relatives) can prevent
  random mixing of genes
• Homozygotes are common in inbred populations.

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Inbreeding in California Sea Otters

• Because inbreeding produces an excess of
  homozygotes in a population, deviations from
  Hardy-Weinberg expectations can be used to detect
  such inbreeding in wild populations.

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Inbreeding in California Sea Otters

• Sea otters, once abundant along the west coast of
  the U.S., were almost wiped out by fur hunters in
  the 18th and 19th centuries.

photo www.turtletrack.org
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Inbreeding in California Sea Otters

• California population reached a low of 50
  individuals (now over 1,500). As a result of
  this bottleneck, the population has less genetic
  diversity than it once had.

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Inbreeding in California Sea Otters

• Population is still at a low density and Lidicker
  and McCollum (1997) investigated whether this
  resulted in inbreeding.
• They determined genotypes of 33 otters for PAP
  locus, which has two alleles S (slow) and F (fast)

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Inbreeding in California Sea Otters

• The genotypes of the 33 otters were
• SS 16
• SF 7
• FF 10
• This gives approximate allele frequencies of S
  0.6 and F 0.4

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Inbreeding in California Sea Otters

• If otter population in H-W equilibrium, genotype
  frequencies should be
• SS 0.6 0.6 0.36
• SF 20.60.4 0.48
• FF 0.40.4 0.16
• However actual frequencies were
• SS 0.485, SF 0.212, FF 0.303

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Inbreeding in California Sea Otters

• There are more homozygotes and fewer
  heterozygotes than expected for a random mating
  population.
• Having considered alternative explanations for
  deficit of heterozygotes, Lidicker and McCollum
  (1997) concluded that sea otter populations show
  evidence of inbreedng.

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Mutation

• Mutation adds new genes, but generally so slowly
  that H-W equilibrium not affected.
• However, mutation and sexual recombination
  ultimately responsible for the variation that
  natural selection depends on.

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Mutations

• Mutations are randomly occurring changes in the
  DNA.
• Only mutations that occur in cell lines that
  produce gametes i.e. the sex cells sperm and
  egg can be passed on.
• Simplest mutation is a point mutation in which
  one base is changed or a base is inserted or
  deleted.

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Mutations

• Changing a base may have no effect if the base
  change does not change the amino acid coded for
  or if the change occurs in a non-coding section
  of the gene.
• However, some changes alter the amino acid coded
  for and hence the protein produced (e.g. as
  occurs in sickle cell anemia), which can have
  severe effects.

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Insertion/deletion mutations

• In insertion/deletion mutations a base is added
  or deleted, which because bases are read in
  groups of three shifts the reading frame so
  that all sequences after the mutation are
  misread, being off by one base.
• This almost always produces a non-functional
  protein

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Mutations that alter gene number or sequence

• Gene duplication is an important source of
  variation.
• In gene duplication a section of DNA may be
  copied and inserted elsewhere in the genome.
  Often these cause major problems, but sometimes
  they do not and the overall number of genes is
  increased. And the new genes can take on novel
  functions through mutation and selection

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Mutations that alter gene number or sequence

• Humans have about 1,000 olfactory receptor genes
  and mice about 1,300. These appear all to have
  been derived from a single ancestral gene.
• In humans about 60 of these are turned off, but
  in mice only about 20 are turned off.

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Sexual Recombination

• In the process of meiosis alleles are reshuffled
  as parental chromosomes exchange portions.
• This process produces new combinations of alleles
  in the sex cells produced in meiosis.
• In addition, the combining of sperm and egg also
  produces new combinations of alleles.

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How populations gene pools are altered

• Natural Selection as discussed previously
  selection for or against allele can cause its
  frequency to change quickly from one generation
  to the next.
• However, natural selection is not the only way
  allele frequencies can change. Chance often
  plays a role.

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Genetic drift

• Fluctuations in allele frequencies that result
  from chance are referred to as genetic drift.
• Chance effects are strongest when populations are
  small. In a small population it is easy for
  alleles to be lost or become fixed as a result of
  chance events.

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Large population size

• If populations are small, chance events can have
  a large effect on allele frequencies.
• These chance events can cause the genetic
  structure to randomly change from one generation
  to the next. This random change is called
  Genetic Drift.

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Genetic Drift events that reduce population size

• Genetic drift is most likely to affect
  populations after events that greatly reduce
  population size.
• Two of the most common are Bottleneck Events and
  Founder Events

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Bottleneck Effect

• A bottleneck effect occurs when some disaster
  causes a dramatic reduction in population size.
• As a result, by chance certain alleles may be
  overrepresented in the survivors, while others
  are underrepresented or eliminated. Genetic
  drift while the population is small may lead to
  further loss or fixation of alleles.

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Bottleneck Effect

• Humans have been responsible for many bottlenecks
  by driving species close to extinction.
• For example, the Northern Elephant seal
  population was reduced to about 20 individuals in
  the 1890s. Population now gt30,000, but an
  examination of 24 genes found no variation, i.e.
  in each case there was only one allele. Southern
  Elephant Seals in contrast show lots of genetic
  variation.

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23.8
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Founder Effect

• When populations are founded by only a few
  individuals (as island communities often are) the
  gene pool is unlikely to be as diverse as the
  source pool from which it was derived.

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Founder Effect

• Founder effect coupled with inbreeding explains
  the high incidence of certain recessive diseases
  among humans in many isolated communities.
• For example, polydactylism (having extra fingers)
  is quite common among the Amish and retinitis
  pigmentosa a progressive form of blindness is
  common among the residents of Tristan da Cunha.

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Natural Selection

• Natural selection is generally the main reason
  populations will deviate from H-W equilibrium.
• With natural selection certain alleles are
  selected against or for and so are are rarer or
  more common than would otherwise be expected in
  the next generation.

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Natural Selection the primary mechanism of
adaptive evolution

• Terms such as survival of the fittest and
  struggle for existence do not necessarily mean
  there is actual fighting for resources.
• Competition is generally more subtle and success
  in producing offspring and thus contributing
  genes to the next generation (i.e. fitness) may
  depend on differences in ability to gather food,
  hide from predators, or tolerate extreme
  temperatures, which all may enhance survival and
  ultimately reproduction

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Natural Selection the primary mechanism of
adaptive evolution

• Three major forms of natural selection
• Directional
• Disruptive
• Stabilizing

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Directional Selection

• Favors one extreme in the population
• Average value in population moves in that
  direction
• E.g. Selection for darker fur color in an area
  where the background rocks are dark

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Disruptive selection

• Intermediate forms are selected against.
  Extremes are favored
• E.g. Pipilo dardanus butterflies. Different
  forms of the species mimic the coloration of
  different distasteful butterflies.
• Crosses between forms are poor mimics and so are
  selected against by being eaten by birds.

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Stabilizing Selection

• Commonest form
• Extreme forms are selected against
• Birth weights in human babies. Highest survival
  is at intermediate birth weights.
• Babies that are too large cannot fit through the
  birth canal, babies that are born too small are
  not well developed enough to survive

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Natural selection acts on individuals, but its
effects accumulate in populations

• Individuals live or die during a the selection
  event.
• But change occurs in the characteristics of the
  population, not in individuals.

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Natural selection acts on individuals,
its effects accumulate in populations

• During a drought on the Galapagos individual
  ground finchs beaks did not change, but the
  populations average beak dimensions changed
  because more small-beaked birds died than
  large-beaked birds.

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Natural selection does not plan ahead.

• Each generation is result of selection by
  environmental conditions of the previous
  generation.
• Evolution always one generation behind
  environmental changes.

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New traits evolve even though selection acts on
existing traits.

• This occurs because
• 1. mutation produces new alleles.
• 2. In sexually reproducing organisms meiosis and
  fertilization recombine existing alleles to
  produce new genotypes.

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New traits evolve even though selection acts on
existing traits.

• Artificial selection for oil content in corn.
• After 60 generations oil levels were well above
  starting values.

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Fig 3.12
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Important points about evolution and natural
selection

• The fundamental unit of natural selection is the
  gene.
• Only genes are passed on from one generation to
  the next.

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Important points about evolution and natural
selection

• Nothing in nature happens for the good of the
  species.
• Alleles that sacrifice themselves would disappear
  from the gene pool.

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Important points about evolution and natural
selection

• Organs must be useful at all stages of their
  evolutionary history
• Structures cannot pass through intermediate
  stages where they make an organism less well
  adapted.

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Important points about evolution and natural
selection

• Natural selection cannot fashion perfect
  organisms for several reasons
• 1. Evolution is limited by historical
  constraints. Birds cannot run around on four
  legs because their forelimbs have evolved into
  wings.

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Important points about evolution and natural
selection

• Natural selection cannot fashion perfect
  organisms for several reasons
• 2. Adaptations are often compromises.
• Auks (a group of seabirds that includes puffins)
  can fly and use their wings to swim underwater,
  but the shape and size of the wing is a
  compromise between the demands of flight and
  swimming.

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Little Auk
polar.alaskapacific.edu/aharding/images/Littl...
Razorbill
http//media-2.web.britannica.com/eb-media/16/2601
6-004-13D8FA4C.jpg
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Important points about evolution and natural
selection

• Natural selection cannot fashion perfect
  organisms for several reasons
• 3. Selection can only make use of the material
  that is available. New alleles do not arise on
  demand.