Instructions for printer-friendly version


x

x

x

x

x

x

x

x

x

x


(photo by John Daniels)

    Evolutionary Force #1: Mutation

    The first factor necessary for evolution to occur is
    • mutation
    • non-infinite population size
    • migration
    • non-random mating
    • natural selection

x

x

x

x

x

x

x

x

x

x


(photo by Steve Dubois)

    Mutation is the Raw Material of Evolution

    Mutation is both
    • the process (= mutagenesis) by which a gene changes to a new allele
    • the end result of that allelic change

    A mutation generates polymorphism:
    more than one form of the trait their gene encodes.

x

x

x

x

x

x

x

x

x

x

    No Polymorphism, No Evolution

    Polymorphism is the existence, in a population,
    of more than one form of a particular trait.

    Polymorphism can be observed at the level of...

    Genotype:
    • alleles at a single locus
    • chromosome number and shape
    • ploidy

    Phenotype:
    • morphology
    • proteins/enzymes
    • immune system components
    A population lacking heritable polymorphism will not evolve.

x

x

x

x

x

x

x

x

x

x

Point Mutations:

Duplication Mutations:

    Mutations Can be
    Small-scale or Large-scale

    Mutations can occur at the level of

      • an individual nucleotide
        • point mutation

      • a short nucleotide sequence
        • duplication
        • deletion
        • inversions
        • translocation
      • a single chromosome
        • duplication
        • deletion
        • inversions
        • translocation

      • a chromosome set
        • polyploidy

x

x

x

x

x

x

x

x

x

x

x

x

x

    Dividing Cells Give Rise to Tissues

    A tissue is defined as an aggregation of cells
    coordinated to perform a particular function or set of functions.

    Only animals and plants have true tissues.

    In a developing plant or animal, stem cells
    can divide and differentiate into any type of cell.

    As a zygote divides, its daughter cells mature and differentiate
    into cells with specific functions in their given tissue.

    Most mature cells lose the capacity for further differentiation.

    Mutations that occur in a dividing cell can be passed to its daughter cells.

x

x

x

x

x

x

x

x

x

x

    Somatic vs. Germline Mutations

    A somatic cell is any cell of a living organism
    except the reproductive cells.

    A germline cell is a reproductive cell.
    A germline cell may

    • undergo meiosis to produce eggs or sperm (animals)
    • undergo meiosis to produce spores (plants, fungi)

    In animals

    • a somatic mutation may affect an individual animal,
      but it cannot be passed to offspring.
    • only a germline mutation can be passed to offspring.

    But is this true in other types of organisms?

x

x

x

x

x

x

x

x

x

x

x

x


(click on pic for source)

    Cellular Potency

    A cell's potency is its ability to differentiate into other cell types.
    The higher the potency, the greater the capacity for differentiation.

    A totipotent cell
    • can differentiate into any type of cell in the organism.
    • can be a
      • zygote (animals, plants)
      • spore (plants)
      • meristem cell (plants)

    A pluripotent cell
    • can develop into any type of embryonic or adult cell
      • (except extra-embryonic membranes in amniote animals)
    • can (normally) be either an
      • embryonic stem cell (gives rise to somatic cells)
      • embryonic germ cell (gives rise to the germline)

    A multipotent cell
    • can develop into specialized cells within its particular tissue
    • cannot develop into cells of other tissues

x

x

x

x

x

x

x

x

x

x

x

x

x


(click on pic for source)

    Determinate vs. Indeterminate Growth

    Determinate growth is growth that stops once a genetically
    pre-determined structure or body has completely formed.
    • An organism or structure exhibiting determinate growth
      will stop growing once it achieves its pre-programmed
      size/stage of development.

    Indeterminate growth does not terminate at a genetically
    pre-determined point.
    • An organism or structure exhibiting indeterminate growth
      will continue to grow throughout its life.

x

x

x

x

x

x

x

x

x

x

Different Organisms, Different Growth Patterns

Living organisms may be
  • unicellular
    • bacteria, archaeans
    • protists
    • some fungi

  • multicellular with determinate growth
    • animals

  • multicellular with indeterminate growth
    • plants
    • most fungi

x

x

x

x

x

x

x

x

x

x

Different Growth Patterns, Different Heritability

x

x

    Prokaryotes

    Bacteria
    • are unicellular
    • reproduce asexually via fission.
    • reproduce sexually via conjugation, transformation, or transduction.
    • DNA present as a single, circular chromosome
    • do not undergo mitosis or meiosis (which occur only in cells with linear chromosomes)
    Any mutations in a bacterial cell can be inherited by daughter cells.

x

    Protists

    Protists
    • are unicellular or colonial.
    • may reproduce sexually or asexually.
    • DNA present as multiple, linear chromosomes
    • reproduce asexually via mitosis
    • reproduce sexually via meiosis
    Any mutations in a unicellular protist can be inherited by daughter cells.

x

x

    Plants

    Plants
    • exhibit indeterminate growth.
    • grow new tissues from totipotent meristem cells all their lives.
    • Meristems can differentiate into germline cells.
    • DNA present as multiple, linear chromosomes
    • reproduce asexually via mitosis
    • produce sexual propagules via meiosis
    In plants, germline mutations in cells derived from meristems are heritable.

x

x

    Fungi

    Fungi
    • exhibit indeterminate growth, but no true tissues.
    • consist of threadlike hyphae containing multiple, haploid nuclei.
    • DNA present as multiple, linear chromosomes
    • reproduce asexually via mitosis
    • produce sexual propagules via meiosis
    • Opposite mating types (+ and -) join to produce diploid zygotes.
    • The zygotes undergo meiosis to form haploid spores.
    In fungi, mutations in hyphal nuclei are potentially heritable

x

x

    Animals

    Animals
    • exhibit determinate growth.
    • have a defined juvenile period.
    • DNA present as multiple, linear chromosomes
    • produce sexual propagules via meiosis
    The animal germline is determined very early in embryo development, and is permanent.
    In animals, only germline mutations are heritable

x

x

x

x

x

x

x

x

x

x

x

x

x

x

    Reproduction: Asexual or Sexual

    Living organisms can reproduce either asexually or sexually.

    Asexual Reproduction

    • offspring produced via mitosis
    • there is only one parent
    • offspring are genetically identical to parent (clones)

    Sexual Reproduction

    • offspring produced via meiosis and fertilization
    • there are two parents
    • offspring are genetically different from both parents

x

x

x

x

x

x

x

x

x

x

    Mutation Provides Variation.
    Sex Spreads it Around

    All differences among alleles arise via mutation.
    But it is sexual reproduction that spreads variation throughout a population.

    • Crossing over creates new combinations of alleles in maternal and paternal chromosomes.

    • Independent assortment of alleles at meiosis provides another source of shuffling phenotypic combinations.

    • Fertilization brings new combinations of shuffled genes and alleles from two different individuals into one individual.

    Each generation of sexual reproduction brings alleles into new combinations.
    This provides an immense variety of allele combinations from any individual making eggs or sperm.

    This kind of diversity is necessary for evolution to occur.

    x

x

x

x

x

x

x

x

x

x

x

    Mutations Can Vary in Phenotypic Effect

    Depending on its location and type, a single mutation can have
    • no phenotypic effect
    • minor phenotypic effect
    • major phenotypic effect
      • resistance to pesticide or antibiotics
      • lethal (usually in homozygous recessive condition)
      • reproductive isolation (e.g., Japanese Land Snail)

x

x

x

x

x

x

x

x

x

x

x

x

    Adaptive, Maladaptive, Neutral

    A mutant allele may be either
    • adaptive - increases the likelihood of survival/reproduction
      in the individual expressing it
    • maladaptive - decreases the likelihood of survival/reproduction
      in the individual expressing it
    • neutral - does not affect the likelihood of survival/reproduction
      in the individual expressing it

x

x

x

x

x

x

x

x

x

x

    Neutral, Silent, and Synonymous Mutations

    • A neutral mutation does not affect its host's Darwininan fitness.

    • A silent mutation
      • changes a triplet codon to a different triplet codon
      • does not change the amino acid encoded in the Genetic Code
      • can occur anywhere in the genome
      • is thus not necessarily translated into protein
      • can still have a phenotypic effect

    • A synonymous mutation
      • is a specific subset of silent mutations
      • changes a triplet codon to a different triplet codon
      • does not change the amino acid encoded in the Genetic Code
      • occurs in an exon
      • is translated into protein

      The terms "silent" and "synonymous" are sometimes used interchangeably,
      but notice the subtle difference between them.

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x


Cognate tRNA frequency correlates to codon use frequency.

    Not Necessarily Neutral

    Silent and synonymous mutations are not necessarily neutral.

    Example #1: Codon bias

    • CCU and CCC both code for the amino acid proline.
    • However, CCU and CCC cognate tRNAs may not be equally abundant.
    • (A cognate tRNA is one whose anticodon is complementary to a particular codon.)
    • In this case, there are several possible effects of a CCU --> CCC mutation:
      • upregulation of protein's synthesis ([GGG tRNA] > [GGA tRNA])
      • downregulation of protein's synthesis ([GGG tRNA] < [GGA tRNA])
      • change in protein conformation due to change in extrusion rate from an idling ribosome

      Each of these could potentially have a phenotypic effect without changing the amino acid sequence.


    Example #2: Changing an intron
    • RNA-editing enzymes recognize and bind specific intron sequences.
    • Altered intron sequence can interfere with binding and proper splicing.
    • A product with altered or disrupted function can result.

    As new information becomes available, we learn that
    mutations once considered "silent" may not be.

x

x

x

x

x

x

x

x

x

x

x

x

x

x

x

    Galapagos Finches: Same Protein, Different Expression

    The different species of Darwin's finches, unique to the Galapagos,
    vary in the size and shape of their bills.

    At least two genes are involved in formation of the bill in the embryo.

    • BMP (Bone Morphogenetic Protein)
      • a family of growth factor proteins
      • discovered for its role in bone formation
      • now known to be involved in widespread control of tissue architecture
      • highly conserved across species

    • CaM (calcium-modulated protein)
      • a family of calcium-binding second messenger proteins
      • involved in many vital animal functions
      • involved in growth and control of cell cycle
      • highly conserved across eukaryotes

    Different, localized upregulation of gene expression
    can generate different shaped bills.

    The lower image shows bill morphogenesis in embryonic finches.
    Dark-staining areas indicate gene expression.
    Red arrows indicate regions of very high concentration of gene product.

    • High levels of BMP4 promote a wide, deep bill.
    • Low levels of BMP4 promote a long, narrow bill.
    • High levels of calmodulin promote a long bill.
    • Low levels of calmodulin promotes a short bill.

    The DNA sequence of the genes themselves has not changed.
    Only the location and degree of expression have changed.

    Upregulation or downregulation of gene expression in a specific tissue
    or body region (compared to an ancestor) can produce significant physical changes.

x

x

x

x

x

x

x

x

x

x

x

x


Recently reported estimates of the human genome-wide mutation rate.
The human germline mutation rate is approximately 0.5 x 10-9/basepair/year. (Click on image for full article.)

    New Mutations Take Up Residence

    Mutation rate is the frequency with which a given gene mutates over time.
    • different genes mutate at different rates
    • those rates are not constant

    Still, genomic mutation rates can be statistically characterized (left).

    Once a mutant allele has appeared, its increase in frequency can be predicted with this:

    (mr) x (ν+)

    Where:
    mr = mutation rate
    ν+ = frequency of the wild type allele

x

x

x

x

x

x

x

x

x

x

In reality, a mutation rate of 1/1000 is unrealistically high.
Mutation rates are much lower in natural populations.
In evolving populations, mutation is usually not the only factor at work.

    A Populational Example

    1. Let's say "Population X" is completely homozygous for gene A.

    2. Allele A mutates into allele a once in every 1000 gametes.
    xx (i.e., A mutates to a at a rate of 0.001)

    3. After a one generation of mutation:
      • Increase in frequency of a = 0.001 x 1.0 = 0.001

          • 0.001 = mutation rate
          • 1.0 = frequency (%) of wild type A available to mutate
          • 0.001 (final product) = frequency of new mutant a allale

    4. The NEW frequency of the wild type A is:
      • 1.0 - 0.001 = 0.999
        • 1.0 initial wild type A allele frequency
        • 0.001 = frequency of new mutant a allele
        • 0.999 = NEW frequency of wild type A allele remaining to mutate

    5. After a second generation of mutation:

      • Increase in frequency of a = 0.001 x 0.999 = 0.000999
          • 0.001 = mutation rate
          • 0.999 = frequency of wild type A allele available to mutate
          • 0.000999 = frequency of new mutant a allale

    6. The NEW frequency of wild type A is:
      • 0.999 - 0.000999 = 0.998
        • 0.999 initial wild type A allele frequency
        • 0.000999 = frequency of new mutant a allele
        • 0.998 = NEW frequency of wild type A allele remaining to mutate

    ...and so on, with each subsequent generation.

    In the absence of other factors, as allele a increases in frequency,
    allele A decreases in frequency.

x

x

x

x

x

x

x

x

x

x

x

x

    The Molecular Clock

    Mutation rate can be used to deduce the time
    since two taxa diverged from a common ancestor.

    A molecular clock is the rate at which a gene (or genome) acummulates mutations.

    In 1962, Emile Zuckerkandle and Linus Pauling published their observation that
    the degree of variation in hemoglobin β-chain amino acid sequence corresponded
    to the phylogenetic distance between the hemoglobin source species.

    This implied that

    • Species/taxa diverge from a common ancestor.
    • Differentiation (evolution) involves accumulation
      of genetic changes between the related species.
    • The longer two species are separate,
      the more different mutations accumulate in their common genes.
    • Distantly related taxa have had time to accumulate
      more evolutionary differences than closely related taxa.
    • If a mutation rate can be established,
      a timeline for evolutionary divergence can be inferred.

x

x

x

x

x

x

x

x

x

x

x

x

x


(click on pic for source)

    What Does the Clock Say?

    The Molecular Clock Hypothesis does NOT imply that:
    • all genes mutate at the same rate
    • all genes are equally suitable to serve as molecular clock genes.

    In reality:

    • Different genes mutate at different rates
    • The rate of mutation of a particular gene can change over time
    • Genes that serve as the most reliable genetic clock markers
      • mutate at a constant rate
      • are not subject to natural selection
      • are often pseudogenes that are no longer functional

x

x

x

x

x

x

x

x

x

x

x

x

    The Molecular Clock Hypothesis

    The Molecular Clock Hypothesis states that
    • DNA evolves at a relatively constant rate over time and among organisms.

    • The genetic difference between any two species is proportional
      to the time since they last shared a common ancestor.

x

x

x

x

x

x

x

x

x

x