Mechanisms of Evolution

1
Mechanisms of Evolution
2
Mechanisms of Evolution

• Key Concepts
• Evolution Is Both Factual and the Basis of
  Broader Theory
• Mutation, Selection, Gene Flow, Genetic Drift,
  and Nonrandom Mating Result in Evolution
• Evolution Can Be Measured by Changes in Allele
  Frequencies
• Selection Can Be Stabilizing, Directional, or
  Disruptive

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Mechanisms of Evolution

• Key Concepts
• Genomes Reveal Both Neutral and Selective
  Processes of Evolution
• Recombination, Lateral Gene Transfer, and Gene
  Duplication Can Result in New Features
• Evolutionary Theory Has Practical Applications

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Evolution Is Both Factual and the Basis of
Broader Theory

• Biological populations change over time, or
  evolve.
• Evolutionary change is observed in laboratory
  experiments, in natural populations, and in the
  fossil record.

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Evolution Is Both Factual and the Basis of
Broader Theory

• Evolutionary theoryunderstanding the mechanisms
  of evolutionary change.
• It has many applications study and treatment of
  diseases, development of crops and industrial
  processes, understanding the diversification of
  life, and how species interact.
• It also allows us to make predictions about the
  biological world.

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Evolution Is Both Factual and the Basis of
Broader Theory

• TheoryIn everyday speech, an untested hypothesis
  or a guess.
• Evolutionary theory is not a single hypothesis,
  but refers to our understanding of the mechanisms
  that result in genetic changes in populations
  over time and to our use of that understanding to
  interpret changes in and interactions among
  living organisms.

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Evolution Is Both Factual and the Basis of
Broader Theory

• Even before Darwin, biologists had suggested that
  species had changed over time, but no one had
  proposed a convincing mechanism for evolution.

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Evolution Is Both Factual and the Basis of
Broader Theory

• Charles Darwin was interested in geology and
  natural history.

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Evolution Is Both Factual and the Basis of
Broader Theory

• In 1831, Darwin began a 5-year voyage around the
  world on a Navy survey vessel, the HMS Beagle.

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Figure 15.1 The Voyage of the Beagle
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Evolution Is Both Factual and the Basis of
Broader Theory

• From the observations and insights made on the
  voyage, and new ideas from geologists on the age
  of the Earth, Darwin developed an explanatory
  theory for evolutionary change
• Species change over time.
• Divergent species share a common ancestor.
• The mechanism that produces change is natural
  selection.

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Evolution Is Both Factual and the Basis of
Broader Theory

• In 1858, Darwin received a paper from Alfred
  Russel Wallace with an explanation of natural
  selection nearly identical to Darwins.
• Both men are credited for the idea of natural
  selection.
• Darwins book, The Origin of Species, was
  published in 1859.

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Evolution Is Both Factual and the Basis of
Broader Theory

• By 1900, the fact of evolution was established,
  but the genetic basis of evolution was not yet
  understood.
• Then the work of Gregor Mendel was rediscovered,
  and during the 20th century, work continued on
  the genetic basis of evolution.
• A modern synthesis of genetics and evolution
  took place 19361947.

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Figure 15.2 Milestones in the Development of
Evolutionary Theory
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Evolution Is Both Factual and the Basis of
Broader Theory

• The structure of DNA was established by 1953 by
  Watson and Crick.
• In the 1970s, technology developed for sequencing
  long stretches of DNA and amino acid sequences in
  proteins.
• Evolutionary biologists now study gene structure
  and evolutionary change using molecular
  techniques.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Biological evolution refers to changes in the
  genetic makeup of populations over time.
• Populationa group of individuals of a single
  species that live and interbreed in a particular
  geographic area at the same time.
• Individuals do not evolve populations do.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• The origin of genetic variation is mutation.
• Mutationany change in nucleotide sequences.
• Mutations occur randomly with respect to an
  organisms needs natural selection acts on this
  random variation and results in adaptation.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Mutations can be deleterious, beneficial, or have
  no effect (neutral).
• Mutation both creates and helps maintain genetic
  variation in populations.
• Mutation rates vary, but even low rates create
  considerable variation.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Because of mutation, different forms of a gene,
  or alleles, may exist at a locus.
• Gene poolsum of all copies of all alleles at all
  loci in a population.
• Allele frequencyproportion of each allele in the
  gene pool.
• Genotype frequencyproportion of each genotype
  among individuals in the population.

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Figure 15.3 A Gene Pool
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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Many of Darwins observations came from
  artificial selection of domesticated plants and
  animals.
• Selection on different characters in a single
  species of wild mustard produced many crop plants.

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Figure 15.4 Many Vegetables from One Species
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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Darwin bred pigeons and recognized similarities
  between selection by breeders and selection in
  nature.

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Figure 15.5 Artificial Selection
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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Laboratory experiments also show genetic
  variation in populations.
• Selection for certain traits in the fruit fly
  Drosophila melanogaster resulted in new
  combinations of genes that were not present in
  the original population.

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Figure 15.6 Artificial Selection Reveals Genetic
Variation
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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Natural selection
• Far more individuals are born than survive to
  reproduce.
• Offspring tend to resemble their parents, but are
  not identical to their parents or to one another.
• Differences among individuals affect their
  chances to survive and reproduce, which will
  increase frequency of favored traits in the next
  generation.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Adaptationa favored trait that evolves through
  natural selection.
• Adaptation also describes the process that
  produces the trait.
• Individuals with deleterious mutations are less
  likely to survive and reproduce and to pass their
  alleles on to the next generation.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Migration of individuals between populations
  results in gene flow, which can change allele
  frequencies.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Genetic driftrandom changes in allele
  frequencies from one generation to the next.
• In small populations, it can change allele
  frequencies. Harmful alleles may increase in
  frequency, or rare advantageous alleles may be
  lost.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• A population bottleneckan environmental event
  results in survival of only a few individuals.
• Genetic drift can change allele frequencies.
• Populations that go through bottlenecks loose
  much of their genetic variation.

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Figure 15.7 A Population Bottleneck
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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Founder effectgenetic drift changes allele
  frequencies when a few individuals colonize a new
  area.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Nonrandom mating
• Selfing, or self-fertilization is common in
  plants. Homozygous genotypes will increase in
  frequency and heterozygous genotypes will
  decrease.

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Sexual selectionmates are chosen based on
  phenotype, e.g., bright-colored feathers of male
  birds.
• There may be a trade-off between attracting mates
  (more likely to reproduce) and attracting
  predators (less likely to survive).

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Mutation, Selection, Gene Flow,Genetic Drift,
and Nonrandom Mating Result in Evolution

• Or, phenotype may indicate a successful genotype,
  e.g., female frogs are attracted to males with
  low-frequency calls, which are larger and older
  (hence successful).
• Studies of African long-tailed widowbirds showed
  that females preferred males with longer tails,
  which may indicate greater health and vigor.

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Figure 15.8 What Is the Advantage?
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Figure 15.9 Sexual Selection in Action (Part 1)
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Figure 15.9 Sexual Selection in Action (Part 2)
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Evolution Can Be Measured by Changes in Allele
Frequencies

• Evolution can be measured by change in allele
  frequencies.
• Allele frequency

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Evolution Can Be Measured by Changes in Allele
Frequencies

• For two alleles at a locus, A and a, three
  genotypes are possible AA, Aa, and aa.
• p frequency of A q frequency of a

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Figure 15.10 Calculating Allele and Genotype
Frequencies
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Evolution Can Be Measured by Changes in Allele
Frequencies

• For each population, p q 1, and q 1 p.
• Genetic structurefrequency of alleles and
  genotypes of a population.

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Evolution Can Be Measured by Changes in Allele
Frequencies

• HardyWeinberg equilibriumallele frequencies do
  not change across generations genotype
  frequencies can be calculated from allele
  frequencies.
• If a population is at Hardy-Weinberg equilibrium,
  there must be no mutation, no gene flow, no
  selection of genotypes, infinite population size,
  and random mating.

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Evolution Can Be Measured by Changes in Allele
Frequencies

• At Hardy-Weinberg equilibrium, allele frequencies
  dont change.
• Genotypes frequencies
• Genotype AA Aa aa
• Frequency p2 2pq q2

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Figure 15.11 One Generation of Random Mating
Restores HardyWeinberg Equilibrium (Part 1)
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Figure 15.11 One Generation of Random Mating
Restores HardyWeinberg Equilibrium (Part 2)
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Evolution Can Be Measured by Changes in Allele
Frequencies

• Probability of 2 A-gametes coming together
• Probability of 2 a-gametes coming together
• Overall probability of obtaining a heterozygote

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Evolution Can Be Measured by Changes in Allele
Frequencies

• Populations in nature never meet the conditions
  of HardyWeinberg equilibriumall biological
  populations evolve.
• The model is useful for predicting approximate
  genotype frequencies of a population.
• Specific patterns of deviation from
  HardyWeinberg equilibrium help identify
  mechanisms of evolutionary change.

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Selection Can Be Stabilizing, Directional, or
Disruptive

• Qualitative traitsinfluenced by alleles at one
  locus often discrete qualities (black versus
  white).
• Quantitative traitsinfluenced by alleles at more
  than one locus likely to show continuous
  variation (body size of individuals).

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Selection Can Be Stabilizing, Directional, or
Disruptive

• Natural selection can act on quantitative traits
  in three ways
• Stabilizing selection favors average
  individuals.
• Directional selection favors individuals that
  vary in one direction from the mean.
• Disruptive selection favors individuals that
  vary in both directions from the mean.

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Figure 15.12 Natural Selection Can Operate in
Several Ways (Part 1)
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Figure 15.12 Natural Selection Can Operate in
Several Ways (Part 2)
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Figure 15.12 Natural Selection Can Operate in
Several Ways (Part 3)
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Selection Can Be Stabilizing, Directional, or
Disruptive

• Stabilizing selection reduces variation in
  populations, but does not change the mean.
• It is often called purifying selectionselection
  against any deleterious mutations to the usual
  gene sequence.

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Figure 15.13 Human Birth Weight Is Influenced by
Stabilizing Selection
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Selection Can Be Stabilizing, Directional, or
Disruptive

• Directional selectionindividuals at one extreme
  of a character distribution contribute more
  offspring to the next generation.
• An evolutionary trend may result.
• Example Texas Longhorn cattle.

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Figure 15.14 Long Horns Are the Result of
Directional Selection
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Selection Can Be Stabilizing, Directional, or
Disruptive

• Disruptive selectionindividuals at opposite
  extremes of a character distribution contribute
  more offspring to the next generation.
• Increases variation in the population can result
  in a bimodal distribution of traits.

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Figure 15.15 Disruptive Selection Results in a
Bimodal Character Distribution
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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Types of mutations
• Nucleotide substitutionchange in one nucleotide
  in a DNA sequence (a point mutation).
• Synonymous substitutionmost dont affect
  phenotype because most amino acids are specified
  by more than one codon.
• Nonsynonymous substitutiondeleterious or
  selectively neutral.

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Figure 15.16 When One Nucleotide Changes (Part 1)
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Figure 15.16 When One Nucleotide Changes (Part 2)
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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Substitution rates are highest at positions that
  do not change the amino acid being expressed.
• Substitution is even higher in pseudogenes,
  copies of genes that are no longer functional.

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Figure 15.17 Rates of Substitution Differ
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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Types of mutations Insertions, deletions, and
  rearrangements
• Can have larger effect than point mutations.
• Can change the reading frame of protein-coding
  sequences.

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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Neutral theoryat the molecular level, the
  majority of variants in most populations are
  selectively neutral.
• Neutral variants must accumulate through genetic
  drift rather than positive selection.
• Suggest a trait that might demonstrate neutral
  variance.
• Why wont neutral variants accumulate through
  natural selection?

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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• The rate of evolution of particular genes and
  proteins is often relatively constant over time,
  and can be used as a molecular clock to
  calculate evolutionary divergence times between
  species.

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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Fitness of genotypes
• Genotypes of higher fitness increase in frequency
  over time those of lower fitness decrease over
  time.

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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Relative rates of substitution types differ as a
  function of selection
• If similar, the corresponding amino acid is
  likely drifting neutrally among states.
• If nonsynonymous substitution exceeds synonymous,
  positive selection results in change in the
  corresponding amino acid.
• If synonymous substitution exceeds nonsynonymous,
  purifying selection resists change in the
  corresponding amino acid.

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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Evolution of lysozyme
• Lysozyme digests bacteria cell walls found in
  almost all animals as a defense mechanism.
• Some mammals are foregut fermenters, which has
  evolved twicein ruminants and leaf-eating
  monkeys (langurs). Lysozyme in these lineages has
  been modified to rupture some bacteria in the
  foregut to release nutrients.

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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Lysozyme-coding sequences were compared in
  foregut fermenters and their non-fermenting
  relatives, and rates of substitutions were
  determined.
• The rate of synonymous substitution in the
  lysozyme gene was much higher than nonsynonymous,
  indicating that many of the amino acids are
  evolving under purifying selection.

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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Replacements in lysozyme happened at a much
  higher rate in langur lineage.
• Lysozyme went through a period of rapid change in
  adapting to the stomachs of langurs.
• Lysozymes of langurs and cattle share five
  convergent amino acid replacements, which make
  the protein more resistant to degradation by the
  stomach enzyme pepsin.

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Figure 15.18 Convergent Molecular Evolution of
Lysozyme (Part 1)
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Figure 15.18 Convergent Molecular Evolution of
Lysozyme (Part 2)
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Genomes Reveal Both Neutraland Selective
Processes of Evolution

• Lysozyme in the crop of the hoatzin, a
  foregut-fermenting bird, has similar adaptations
  as those of langurs and cattle.

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Genomes Reveal Both Neutral and Selective
Processes of Evolution

• Heterozygotes can be advantageous as
  environmental conditions change, and polymorphic
  loci are maintained.
• Colias butterflies live in an environment with
  temperature extremes. The population is
  polymorphic for an enzyme that influences flight
  at different temperatures.
• Heterozygotes are favored because they can fly
  over a larger temperature range.

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Figure 15.19 A Heterozygote Mating Advantage
(Part 1)
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Figure 15.19 A Heterozygote Mating Advantage
(Part 2)
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Genomes Reveal Both Neutral and Selective
Processes of Evolution

• Genome size and organization also evolves.
• Genome size varies greatly.
• If only the protein and RNA coding portions of
  genomes are considered, there is much less
  variation in size.

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Figure 15.20 Genome Size Varies Widely
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Figure 15.21 A Large Proportion of DNA Is
Noncoding
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Genomes Reveal Both Neutral and Selective
Processes of Evolution

• Much of the noncoding DNA does not appear to have
  a function.
• Some noncoding DNA can alter the expression of
  surrounding genes.
• Some noncoding DNA consists of pseudogenes.
• Some consists of parasitic transposable elements.

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Genomes Reveal Both Neutral and Selective
Processes of Evolution

• The amount of nonconding DNA may be related to
  population size.
• Noncoding sequences that are only slightly
  deleterious are likely to be purged by selection
  most efficiently in species with large population
  sizes.
• In small populations genetic drift may overwhelm
  selection against these sequences.

85
Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• Sexual reproduction results in new combinations
  of genes and produces genetic variety that
  increases evolutionary potential.
• But in the short term, it has disadvantages
• Recombination can break up adaptive combinations
  of genes
• Reduces rate at which females pass genes to
  offspring
• Dividing offspring into genders reduces the
  overall reproductive rate

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• Why did sexual reproduction evolve? Possible
  advantages
• It facilitates repair of damaged DNA. Damage on
  one chromosome can be repaired by copying intact
  sequences on the other chromosome.
• Elimination of deleterious mutations through
  recombination followed by selection.

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• In asexually reproducing species, deleterious
  mutations can accumulate only death of the
  lineage can eliminate them
• Muller called this the genetic ratchetmutations
  accumulate or ratchet up at each replication
  Mullers ratchet.

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• The variety of genetic combinations in each
  generation can be advantageous (e.g., as defense
  against pathogens and parasites).
• Sexual recombination does not directly influence
  the frequencies of alleles. Rather, it generates
  new combinations of alleles on which natural
  selection can act.

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• Lateral gene transferindividual genes,
  organelles, or genome fragments move horizontally
  from one lineage to another.
• Species may pick up DNA fragments directly from
  the environment.
• Genes may be transferred to a new host in a viral
  genome.
• Hybridization results in the transfer of many
  genes.

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• Lateral gene transfer can be advantageous to a
  species that incorporates novel genes.
• Genes that confer antibiotic resistance are often
  transferred among bacteria species.

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• Gene duplicationgenomes can gain new functions.
• Gene copies may have different fates
• Both copies retain original function (may
  increase amount of gene product).
• Gene expression may diverge in different tissues
  or at different times in development.

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

1. One copy may accumulate deleterious mutations and
   become a functionless pseudogene.
2. One copy retains original function, the other
   changes and evolves a new function.

93
Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• Sometimes entire genomes may be duplicated,
  providing massive opportunities for new functions
  to evolve.
• In vertebrate evolution, genomes of the jawed
  vertebrates have 4 diploid sets of many genes.
• Two genome-wide duplication events occurred in
  the ancestor of these species. This allowed
  specialization of individual vertebrate genes.

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Recombination, Lateral Gene Transfer,and Gene
Duplication Can Result in New Features

• Successive rounds of duplication and sequence
  evolution may result in a gene family, a group of
  homologous genes with related functions.
• The globin gene family probably arose via gene
  duplications.

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Figure 15.22 A Globin Family Gene Tree
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Evolutionary Theory Has Practical Applications

• Molecular evolutionary principles are used to
  understand protein structure and function.
• Puffer fish have a toxin (TTX) that blocks sodium
  ion channels and prevents nerve and muscle
  function.
• Genes for sodium channel proteins in puffer fish
  have substitutions that prevent TTX from binding.
• Study of these gene substitutions aid in
  understanding how sodium channels function.

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Evolutionary Theory Has Practical Applications

• Living organisms produce many compounds useful to
  humans. The search for such compounds is called
  bioprospecting.
• These molecules result from millions of years of
  evolution.
• But biologists can imagine molecules that have
  not yet evolved. In vitro evolutionnew molecules
  are produced in the laboratory to perform novel
  functions.

98
Evolutionary Theory Has Practical Applications

• In agriculture, breeding programs have benefited
  from evolutionary principles, including
  incorporation of beneficial genes from wild
  species.
• An understanding of how pest species evolve
  resistance to pesticides has resulted in more
  effective pesticide application and rotation
  schemes.

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Evolutionary Theory Has Practical Applications

• Molecular evolution is also used to study disease
  organisms.
• All new viral diseases have been identified by
  evolutionary comparison of their genomes with
  those of known viruses.

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Figure 15.24 Evolutionary Analysis of Surface
Proteins Leads to Improved Flu Vaccines