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Molecular and Genomic Evolution

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Title: Molecular and Genomic Evolution


1
Molecular and Genomic Evolution
2
Molecular and Genomic Evolution
  • Genomes and Their Evolution
  • The Evolution of Macromolecules
  • Determining and Comparing the Structure of
    Macromolecules
  • Proteins Acquire New Functions
  • The Evolution of Genome Size
  • The Uses of Molecular Genomic Information

3
Genomes and Their Evolution
  • An organisms genome is the full set of genes it
    contains.
  • In eukaryotes, most of the genes are found in the
    nucleus, but genes are also present in plastids
    and chloroplasts.
  • Genes are shuffled in every generation of
    sexually reproducing organisms via meiosis and
    fertilization.

4
Genomes and Their Evolution
  • For a gene to be passed on to successive
    generations, the individual with that gene must
    survive and reproduce.
  • A genes capacity to cooperate with different
    combinations of other genes will likely increase
    its probability of transmission.
  • The genes of an individual can be viewed as
    interacting members of a group in which there are
    divisions of labor and strong interdependencies.

5
Genomes and Their Evolution
  • Studies of genomic evolution look at the genome
    of an organism as an integrated whole and attempt
    to answer questions such as
  • How do proteins acquire new functions?
  • Why are the genomes of different organisms so
    variable in size?
  • How has the enlargement of genomes been
    accomplished?

6
The Evolution of Macromolecules
  • The molecules of interest to molecular
    evolutionists are nucleotides, nucleic acids,
    amino acids, and proteins.
  • Molecular evolutionists investigate the evolution
    of these macromolecules to determine how rapidly
    they change and why they have changed.
  • Knowledge of the rate of change of a given
    macromolecule is crucial to attempts to
    reconstruct the evolutionary history of groups of
    organisms.

7
The Evolution of Macromolecules
  • Nucleic acids evolve when nucleotide base
    substitutions occur.
  • Substitutions can change the amino acid sequence,
    and thus the structure and function, of the
    polypeptides.
  • By characterizing nucleic acid sequences and the
    primary structures of proteins, molecular
    evolutionists can determine how rapidly these
    macromolecules have changed and why they changed.

8
The Evolution of Macromolecules
  • Molecular evolution differs from phenotypic
    evolution in one important way In addition to
    natural selection, random genetic drift and
    mutation exert important influences on the rates
    and directions of molecular evolution.
  • A mutation is any change in the genetic material.

9
The Evolution of Macromolecules
  • Many mutations, called silent or synonymous
    mutations, do not alter the proteins they encode.
  • This is because most amino acids are specified by
    more than one codon in the universal genetic
    code.
  • For example, leucine is specified by six
    different codons UUA, UUG, CUU, CUC, CUA, and
    CUG.
  • Since silent mutations are unlikely to be
    influenced by natural selection, they are free to
    accumulate in a population over time at rates
    determined by rates of mutation and genetic drift.

10
The Evolution of Macromolecules
  • A nonsynonymous mutation does change the amino
    acid sequence.
  • For example, UUA to UUC would result in a
    phenylalanine rather than a leucine in the
    protein.
  • Nonsynonymous mutations are usually deleterious,
    but those that dont alter the proteins shape
    may be selectively neutral.
  • Most natural populations of organisms harbor much
    more genetic variation than would be expected if
    genetic variation were influenced primarily by
    natural selection.

11
Figure 26.1 When One Base Does or Doesnt Make a
Difference
12
The Evolution of Macromolecules
  • In 1968, Motoo Kimura proposed the neutral theory
    of molecular evolution.
  • The neutral theory postulates that, at the
    molecular level, the majority of mutations are
    selectively neutral.
  • If so, the majority of evolutionary changes in
    macromolecules, and much of the genetic variation
    within species, result from neither positive
    selection of advantageous alleles nor stabilizing
    selection, but from random genetic drift.

13
The Evolution of Macromolecules
  • Using the rationale that the rate of fixation of
    mutation is theoretically constant and equal to
    the neutral mutation rate, the concept of the
    molecular clock was developed.
  • The concept of the molecular clock states that
    macromolecules should diverge from one another at
    a constant rate.

14
Determining and Comparing theStructure of
Macromolecules
  • Biologists must determine the precise structure
    of macromolecules to investigate patterns of
    molecular evolution.
  • PCR allows biologists to amplify ancient DNA to
    concentrations that can be used in experiments to
    determine its sequence.
  • When the amino acid sequences of proteins from
    different organisms have been determined, they
    can be compared by sequence alignment.

15
Figure 26.2 Amino Acid Sequence Alignment (Part
1)
16
Figure 26.2 Amino Acid Sequence Alignment (Part
2)
17
Determining and Comparing theStructure of
Macromolecules
  • Once the amino acid sequences have been aligned,
    they can be compared.
  • A similarity matrix can be constructed by adding
    up the number of similar and different amino
    acids in the sequences.
  • The longer the molecules have been evolving
    separately, the more differences they will have.
  • Substitution rates are highest at codon sites
    that do not change the amino acid being
    expressed, and in pseudogenes.

18
Figure 26.3 Rates of Base Substitution Differ
19
Determining and Comparing theStructure of
Macromolecules
  • The much slower rate of mutation at sites that do
    affect molecular function is consistent with the
    view that most nonsynonymous mutations are
    disadvantageous and are eliminated from the
    population by natural selection.
  • In general, the more essential a molecule is for
    cell function, the slower the rates of its
    evolution.
  • A molecule that illustrates this principle is the
    enzyme cytochrome c, a component of the
    respiratory chain in mitochondria.

20
Figure 26.4 Amino Acid Sequence of Cytochrome c
(Part 1)
21
Figure 26.4 Amino Acid Sequence of Cytochrome c
(Part 2)
22
Determining and Comparing theStructure of
Macromolecules
  • To function as a molecular clock, a macromolecule
    would need to evolve at an approximately constant
    rate in all evolutionary lineages.
  • Cytochrome c sequences have evolved at a
    relatively constant rate.
  • Many other proteins show similar consistency in
    the rate at which they have changed over time,
    but not all molecules change at the same rate.

23
Figure 26.5 Cytochrome c Has Evolved at a
Constant Rate
24
Determining and Comparing theStructure of
Macromolecules
  • Organisms with short generation times generally
    have faster rates of molecular evolution than
    organisms with longer generation times.
  • Shorter generations result in more rounds of DNA
    replication and thus more opportunity for errors
    in replication.
  • The rate of substitution per base per year in
    introns is 2 to 4 times greater in rodents than
    in primates.

25
Proteins Acquire New Functions
  • Evolution would not have been possible if
    proteins were unable to change their functional
    roles.
  • Evidence indicates that all living organisms
    arose from a single ancestral lineage.
  • Thus the many thousands of different functional
    genes that exist today must have arisen from a
    small number of ancestral genes.

26
Proteins Acquire New Functions
  • The most important process enabling proteins to
    acquire new functions appears to be gene
    duplication.
  • Gene duplication may involve part of a gene, a
    single gene, parts of a chromosome, or whole
    chromosomes.
  • Polyploidy, the duplication of an entire genome,
    has been important in speciation.
  • Autopolyploid individuals avoid imbalances in
    gene expression because all of their chromosomes
    are duplicated.

27
Proteins Acquire New Functions
  • Evolution of a new function for a protein
  • Lysozyme is an enzyme found in almost all
    animals it digests bacterial cell walls and is
    the first line of defense against invading
    bacteria.
  • In mammals, a mode of digestion known as foregut
    fermentation has evolved twice. Bacteria in the
    foregut break down ingested plant matter by
    fermentation.
  • In foregut fermenting animals, lysozyme has been
    modified to play a nondefensive role.
  • The enzyme ruptures some of the bacteria that
    live in the foregut, releasing nutrients that the
    animal absorbs.

28
Table 26.1 Similarity Matrix for Lysozyme in
Mammals
29
Proteins Acquire New Functions
  • Five amino acid substitutions are shared by
    foregut fermenters (cow and langur).
  • The substitutions make it more resistant to the
    pancreatic enzyme trypsin and the acidic
    conditions of the stomach.
  • Similar substitutions of hoatzin lysozyme have
    occurred to provide a similar function as cow and
    langur lysozyme.
  • These three groups of animals independently
    evolved a similar molecule that enables them to
    recover nutrients from their fermenting bacteria.

30
The Evolution of Genome Size
  • The size and composition of the genomes of many
    species show much variation.
  • Multicellular organisms have more DNA than
    single-celled organisms.
  • Generally, more complex organisms have more DNA
    than less complex organisms.

31
Figure 26.7 Complex Organisms Have More Genes
than Simpler Organisms
32
The Evolution of Genome Size
  • Some of the apparent differences in genome size
    disappear when the portion of DNA that actually
    codes for RNA or protein is compared.
  • The size of the coding genome varies in a way
    that makes sense
  • Eukaryotes have more coding DNA than
    prokaryotes.
  • Plants have more than single-celled organisms.
  • Vertebrates have more than nonvertebrates.

33
The Evolution of Genome Size
  • Most of the variation in genome size is due to
    the amount of noncoding DNA an organism has.
  • Much of the noncoding DNA may consist of
    pseudogenes that are carried with the genome
    because the cost of doing so is small.
  • Some of the DNA consists of transposable elements
    that spread through populations because they
    reproduce faster than the host genome.

34
Figure 26.8 A Large Proportion of DNA Is
Noncoding
35
The Evolution of Genome Size
  • Retrotransposons are being used by scientists to
    determine the rates at which species lose DNA.
  • The most common type carries long terminal
    repeats (LTRs) at each end.
  • Occasionally, LTRs join together in the host
    genome, causing the DNA between them to be
    excised and leaving one of the LTRs behind.
  • The number of these orphaned LTRs in a genome
    is a measure of how many retrotransposons have
    been lost.
  • Scientists can use the number of LTRs present in
    the genomes of different organisms to compare
    their rates of DNA loss.

36
The Evolution of Genome Size
  • Two identical copies of a gene can have one of
    three different fates
  • Both copies may retain their original function.
  • One copy may become incapacitated by the
    accumulation of deleterious mutations and become
    a pseudogene.
  • One copy may retain its original function while
    the other accumulates enough mutations that it
    can perform a different function.
  • The third is the most significant for evolution.

37
The Evolution of Genome Size
  • The frequency of gene duplications and their
    outcome can be assessed by counting the number of
    synonymous nucleotide base changes in the genome
    and then comparing that with the number of base
    changes causing protein alterations.
  • The rates of gene duplication are fast enough for
    a yeast or Drosophila population to acquire
    several hundred duplicate genes over the course
    of a million years.
  • Although most duplicate genes disappear rapidly
    on an evolutionary time scale, some duplications
    lead to the evolution of genes with new functions.

38
The Evolution of Genome Size
  • Several rounds of duplication and mutation may
    lead to formation of a gene family, a group of
    homologous genes with related functions.
  • There is evidence that the globin gene family
    arose by gene duplication.
  • To estimate the time of the first globin gene
    duplication, a gene tree can be created.
  • Based on the gene tree, the two globin gene
    clusters are estimated to have split about 450
    mya.

39
Figure 26.9 A Globin Family Gene Tree
40
The Uses of Molecular Genomic Information
  • Molecules that have evolved slowly can be used to
    estimate relationships among organisms that
    diverged long ago.
  • Molecules that have evolved rapidly are useful
    for studying organisms that share recent common
    ancestors.
  • To determine the molecular evolutionary
    relationships of all existing animals, a molecule
    that all organisms possess must be used, such as
    rRNA.

41
The Uses of Molecular Genomic Information
  • rRNA has evolved very slowly because even minor
    changes in its base sequence result in inactive
    ribosomes.
  • Differences among the rRNAs of living organisms
    can be used to estimate the timing of lineage
    splits.
  • Molecular, morphological, and fossil data are
    regularly used in combination to create a
    phylogeny.
  • The more characters that are used to create a
    phylogeny, the more accurate it will be.

42
The Uses of Molecular Genomic Information
  • Genes found in different organisms that arose
    from a single gene in their common ancestor are
    called orthologs.
  • Genes that are related through gene duplication
    events in a single lineage are called paralogs.
  • All of the genes in the engrailed gene family are
    orthologs.
  • Paralogous engrailed genes have been generated in
    some lineages as a result of duplication events.

43
Figure 26.10 Phylogeny of the Engrailed Genes
44
The Uses of Molecular Genomic Information
  • Understanding the genomes of pathogens and the
    organisms that carry them has already had medical
    benefits.
  • The determination of the genomes of Anopheles and
    Plasmodium has allowed scientists do develop
    transgenic mosquitoes that express an
    anti-Plasmodium molecule that makes them
    inefficient vectors of malaria in the lab.
  • Information provided by the genomic sequence of
    Treponema pallidum, the bacterium that causes
    syphilis, is being used to develop a vaccine
    against this disease.

45
The Uses of Molecular Genomic Information
  • The AIDS epidemic reminds us that molecular data,
    while providing powerful tools in our struggle
    with diseases, cannot solve all medical problems.
  • A highly active antiretroviral therapy (HAART) is
    generally used to treat AIDS patients.
  • Unfortunately, strains of resistant HIV develop
    in the blood of most patients that receive HAART.
  • The combination of a high mutation rate and no
    repair mechanism means that a new mutant is
    generated every time HIV replicates its genome.

46
The Uses of Molecular Genomic Information
  • Scientific understanding of the evolutionary
    patterns of life on Earth and how the agents of
    evolution governed those patterns is advancing
    more rapidly than ever.
  • By combining molecular data with information from
    the fossil record, biologists are developing an
    increasingly comprehensive picture of the
    evolution of life on Earth.
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