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Microevolution: Genetic Change Within Populations

  • Individual organisms do not evolve in a single lifetime.
  • Populations evolve over generations.
  • Evolution is the result of natural selection at the level of the gene.
  • This idea first proposed by William D. Hamilton in his work on the evolutionary underpinnings of altruism.

  • Professor Richard Dawkins, whom you have met before, made this idea accessible in his book The Selfish Gene.


  • Bonus: (Meet Professor Richard Dawkins.)

    To better understand this all-important concept, let's start with...

    A Glossary of Terms (a review)

    • evolution: change over time

    • organic evolution: change in living organisms over time
      • microevolution - genetic change within a species over generations
      • macroevolution - evolution above the species level
        • reproductive isolation within a population resulting in two new species
        • diversification of major lineages of organisms
        • evolution on a "grand scale"
          • stasis (species existing for a long time without change)
          • modification (change in traits over time)
          • speciation (reproductive isolation)
          • extinction (it's forever)

      • population: all individuals of the same species living in a defined geographic (or smaller, organismal) area.

      • deme - a local, actively interbreeding population that shares a distinct gene pool. (Isolation of a deme from other conspecific demes can result in the generation of subspecies (microevolution) or, sometimes, speciation (macroevolution)).

      • gene pool: all the genes at all loci in every member of an interbreeding population.

      • adaptation - This term has different definitions in physiology vs. evolutionary biology:

        • physiological adaptation - a short term change in physiology, morphology, metabolism, etc. made by an individual organism in response to environmental changes, such as...

          • a mammal seasonally changing fur color and density

          • the pupillary reflex

        • evolutionary adaptation - can be either:
          • the process by which a population evolves to become better suited to its environment
          • a character/trait that has resulted from the evolutionary process
            • example: The fusiform/torpedo shape of a dolphin is better suited for swimming than that of its terrestrial, tetrapod relatives.


            • example: Mammals have evolved dentition most effective at handling their particular diet.

    Physiological adaptations are relatively short-term responses--driven by changes in gene expression--to environmental challenges.

    The capacity to undergo various physiological adaptations is the product of evolutionary adaptation.

    An individual organism may adapt to its environment given the limits of what evolution has bequeathed it, but an individual organism does not evolve.



    What Causes a Population to Evolve?

    The genetic makeup of a population can change by means of five mechanisms:
    • mutation
    • small population size
    • non-random (assortative) mating
    • migration into or out of the population
    • natural selection

    We will consider each of these in turn.


    1. Mutation

    The raw material of evolution is mutation, defined as
    • the process by which a gene changes from one allele to another
    • the end result of that allelic change
    Depending on the nature and location of a mutation, even a small genetic change can have major phenotypic consequences.

    Without genetic variation, there can be no evolution.

    Hence, an asexual clone (defined as a group of genetically identical organisms) should not evolve.

    (Can you think of any way that a clone might begin to evolve?)


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

    If these multiple phenotypes are heritable, and result from different alleles (products of mutation) at a particular locus or interacting loci, then they are subject to the forces of evolution.

    Polymorphism can be seen at many levels:

      1. morphological polymorphism - variation in physical characteristics (color, size, pattern, etc.)

      • flower color in Claytonia...

      • skin pattern in garter snakes...

      • variety in our own species...

        Consider an example of polymorphism in our own species: wisdom teeth

      (Recall the implication of polymorphism of a trait in a natural population.)



    2. chromosomal polymorphism - karyotype is usually species specific. However, non-lethal anomalies may be common among the members of a population. Chromosomal polymorphisms among individuals of the same species can be due to

    3. immunological polymorphism - antigen specificities may vary within and among populations.

    4. protein polymorphisms - codon change --> protein change

    5. DNA polymorphisms, such as:

    • restriction site variation - variation in location of a restriction sequences among individuals.
      (These are detectable via the activity of restriction endonucleases.)

    • tandem repeats - multiplied repeats of a particular DNA sequence

    • complete sequence variation - electrophoretically distinguishable classes of genes that differ at a single position (single-nucleotide polymorphism (SNP)).

    • polymorphism in a single gene locus at different positions - Genes can also vary in their polymorphism at different locations.
      Note: Less variation (among related species) at a particular position of the gene indicates that the position has not tolerated mutation. The variation has been restricted because that region's conformation in the active polypeptide may not be functional if changed, even slightly. Hence, any mutations at that position would be maladaptive, and not as likely to be passed on as mutations at less critical positions on the gene.


    Mutations and Evolution: Location, Location, Location

    In animals, every nucleate, diploid cell contains two copies of the genome, one from each parent.
    Only very specific cells are ever passed on to the next generation.

    • germline cells give rise to gametes
    • somatic cells make up the body itself

    Mutations can happen in either germline or somatic cells, but--in animals--only germline mutations can be passed on to the next generation.

  • If a (germline) gene mutates, a new allele is potentially added to the gene pool.
  • Whether that mutation remains in the population depends on both random and non-random factors.

    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

    Mutations Vary in Phenotypic Effect

    • no significant phenotypic effect
      • occurs in a non-functional region of the genome
      • does not change the encoded amino acid (silent mutation)
      • Note of Caution: a silent mutation may not always be a neutral mutation.
        • a silent mutation does not change the identity of the encoded amino acid
        • a neutral mutation does not affect the Darwininan fitness of the organism expressing it.
        • nucleotide sequence can affect the secondary structure of DNA and hence, its activity, OR
        • tRNAs bearing different anticodons for the same amino acid may not be present with equal frequency in the cell, a silent mutation can affect the rate of translation of proteins containing that amino acid. (This codon bias may prevent a silent mutation from being neutral.)
        • A change in the availability of a particular amino acid during translation can have a profound effect on phenotype, as we will see in a later lecture.

    • small phenotypic effect
      • a minor change may or may not affect Darwinian fitness

    • major phenotypic effect
      • a single mutation can result in resistance to pesticide or antibiotics
      • a single mutation can be lethal (usually in homozygous recessive condition)
      • sometimes a single mutation can cause reproductive isolation, as in the Japanese Land Snail.

        If a mutation causes reproductive isolation, other factors can contribute to further differentiation in the now separate gene pools over time.

    Cell Capacity for Differentiation: Evolutionary Effects

    Cell division is a simple matter of mitosis, but in an embryo this division follows a set pattern of cleavages.

    As animal embryonic cells (blastomeres) divide and mature, they become less versatile in terms of their fate:

    • A totipotent cell has the capacity to develop into any type of cell, whether embryonic, extra-embryonic (amnion, chorion, allantois), or adult.
      The zygote, and possibly the blastomeres of the first few cleavages in deuterostomes, are the only truly totipotent cells.

    • A pluripotent cell can develop into any type of adult cell, but cannot give rise to extra-embryonic membranes (amnion, chorion, allantois).
      Three types of pluripotent cells are known:
      • embryonic stem cells (give rise to the somatic cells)
      • embryonic germ cells (give rise to the germline)
      • embryonic carcinoma cells (abnormal, aneuploid cells found in embryonic teratocarcinomas (germ cell tumors).

    • A multipotent cell can develop into multiple types of cells, but not as many types as a pluripotent cell. These stem cells usually give rise to cells in a particular type of tissue.
      Example: a hematopoietic cell can give rise to various types of blood cells (red blood cells, white blood cells, platelets, etc.), but not to muscle or liver cells.


    With different levels of cell developmental potency in mind, let's consider the evolutionary significance of somatic vs. germline mutations in...

      Animals

      • Animals exhibit determinate growth.
      • This means that there is a defined juvenile period.
      • At the onset of sexual maturity, somatic growth slows dramatically or stops.
      • The germline is determined early in development.
      • Only germline mutations are heritable

      Plants

      • Plants exhibit indeterminate growth.
      • This means they grow new tissues from embryonic (meristem) cells all their lives.
      • Meristematic cells remain pluripotent throughout the plant's life.
      • Meristem cells give rise to new roots and shoots.
      • New shoots give rise to germline cells.
      • Mutations in the new, meristem-derived germline may be passed to offspring.

      Fungi

      • Fungi exhibit indeterminate growth.
      • Fungi consist of threadlike hyphae containing haploid nuclei.
      • When reproducing sexually, hyphae of opposite mating types (+ and -) join to form a fruiting body.
      • Inside, the haploid nuclei of opposite types fuse to form diploid zygotes.
      • The zygotes undergo meiosis to form haploid spores.
      • If there are mutations during meiosis, then any of the new haploid hyphae growing from the mutant spores could pass on those mutations.

      Protists

      • A single-celled organism can still undergo mutation when it undergoes mitosis.
      • Though not a product of sexual recombination, such mutations are nevertheless inherited by the mutant cell's descendants.
      • Many protists have sexual cycles, and mutations can be passed on in this way, as well.

      Prokaryotes

      • Bacteria are generally haploid, but their DNA can mutate during replication.
      • Mutations in a bacterial cell will be passed on to descendant cells.
      • Bacteria can exchange genetic material during conjugation, transformation, or transduction, and mutations can be shared in this way, as well.


    Types of mutations

    As cells prepare to divide via mitosis (asexual) or meiosis (sexual), DNA is replicated to provide copies of the genome to each new daughter cell. Mistakes can happen, either spontaneously or due to environmental factors (mutagens).

    Mutations can occur at the level of

    • individual nucleotides
    • short sequences of nucleotides
    • the chromosome
    • the chromosome set

    1. Mutations at the Nucleotide Level
    Molecular mutations are those that occur at the level of the DNA molecule. Small changes can have profound effects on the phenotype of the organism inheriting that change. The simplest type of molecular mutation is the point mutation, an error in a single DNA base.

    2. Mutations at the Chromosomal Level

    Chromosomal mutations (which also change the DNA sequence at a more expansive level) are those that can be seen at the chromosome level.
    They may include

    • Chromosome breakage resulting in
      • deletion of chromosome segments/genes
      • duplication of chromosome segments/genes
      • rearrangement of chromosome segments (inversions)
      • Chromosomes swapping pieces with each other (translocations)

    • Deletions or additions of entire chromosomes (aneuploidies)
      • euploidy: "true" ploidy, meaning the normal, two members of each homologous pair are present
      • aneuploidy: "not true" ploidy, meaning more or fewer members than two of each homologous pair are present
        • monosomy - only one member of a homologous pair is present
        • trisomy - three homologs (one too many)

        • nullisomy - one entire homologous pair is missing


    3. Mutations at the Chromosome Set Level

  • a cell with one set of nuclear chromosomes is haploid
  • a cell with two sets of nuclear chromosomes is diploid
  • a cell with more than two sets of nuclear chromosomes is polyploid

    Haploid Organisms

    Many mature organisms live most or all of their life as haploids. Bacteria, algae and fungi are good examples.

    All plants undergo alternating generations in which a sporophyte individual (diploid) produces haploid (gametophyte) offspring, and these haploid gametophytes produce diploid (sporophyte) offspring, and so on, in alternation.

    Haploidy is a normal condition in some animal species, such as honeybees (drones)--where it takes part in sex determination--but it is not very common in animals.

    Diploid Organisms

    Until recently, it has traditionally been thought that the vast majority of organisms are diploid, with one genome coming from mom, and the other from dad.

    But sometimes "diploidy" is just a convenient definition. Many organisms currently considered to be diploid are probably the descendants of ancient ancestors who changed in one generation by inheriting multiple chromosome sets from their parents.

    Polyploid Organisms

    Until relatively recently, polyploidy was believed to be uncommon except in flowering plants, in which it is known to be a major mechanism of speciation.

  • autopolyploidy results when extra chromosome sets all come from the same species

  • allopolyploidy - extra chromosome set from a different species.

  • A hybrid is an organism produced by genetically dissimilar parents.

    Hybridization and the resulting polyploidy (<--This is a required-reading link.) may be a more common (if ancient) means of speciation than evolutionary biologists once thought.

    Polyploid individuals are often larger and physically more robust than the parents.

    Both plants above are the same species of Bacopa, and the same age. The one on the right is diploid, and the one on the left is tetraploid.

    The large, seedless, domestic bananas we eat today are descended (via artificial selection) from polyploid hybrids of two wild diploid species, Musa acuminata and M. balbisiana.

    The wild banana is small, sour, and full of pea-sized seeds.



    What Determines Whether a Mutation "Sticks" in a Population?

    Several models/theories have been proposed to explain how and why a mutation might become resident in a population.

    The Classical Model

    In any given population, one allele functions better than the others at a particular locus.
    Natural selection will drive the population to a higher proportion of this allele.
    • The most common phenotype (for a particular trait) in a (natural) population is known as the wild type phenotype.
    • Wild type is often designated as "+" in genetic shorthand.
    • Any allele other than the wild type is said to be mutant.
    • Examples of wild type traits in various species:

    Mutant alleles of these genes may be adaptive, maladaptive, or neutral, depending on circumstances.
    • Tigers: white, not to be confused with albino
    • Leopards: wild type and melanistic (The fabled "black panther" is just a melanistic leopard or jaguar.)
    • Humans have their own array of unusual mutations, and here are just a few.

  • Change of a wild type allele to a mutant allele is known as a forward mutation.
  • Change of a mutant allele back to wild type is known as a reverse mutation or reversion mutation.
  • At a given gene locus, mutational equilibrium is attained when forward and reverse mutations occur at the same rate.
  • The larger the population, the more chances for mutations to occur.

  • Depending on many factors, a mutant allele could foster a new wild type if the resulting phenotype is sufficiently adaptive in the particular environmental context.

    The Balancing Selection Model

    Under certain circumstances, multiple alleles at a particular locus can be retained in the gene pool if an allele that is maladaptive under certain conditions is adaptive under different conditions.

    Theodosius Dobzhansky coined the term balancing selection to describe this phenomenon.

    Balancing selection can prevent one adaptive allele from completely displacing others, thus generating balanced polymorphism: the maintenance of stable frequencies of two or more phenotypic forms in a population.

    Two of the best-known mechanisms by which Balancing Selection operates

      1. HETEROZYGOTE ADVANTAGE - heterozygosity confers a selective advantage over homozygosity, keeping a "maladaptive" allele in the population.
      • Sickle Cell Anemia
        The recessive allele, highly deleterious in homozygous condition, is not cleared from the population because when it occurs in heterozygous condition, it confers immunity to malaria. A balanced polymorphism of the SS, Ss and ss phenotypes occurs in natural populations in Western Africa where malaria is prevalent.

      • Male Homosexuality in Humans
        While genes encoding homosexuality have been identified, this study found that female maternal relatives of male homosexuals have higher fecundity than female maternal relatives of male heterosexuals. (This difference was not found in female paternal relatives.)

        Could heritable alleles that predispose a male to homosexuality be adaptive when they occur in females?

      2. FREQUENCY-DEPENDENT SELECTION - in which selective pressure against a particular allele changes with that allele's relative frequency in the population.

        Predators often develop a search image for particular prey items.
        • When a predator develops knowledge of what a certain preferred type of prey looks like, smells like, etc., then that predator's sensory systems develop a sensitivity and preference for that shape, color, size, smell, etc.
        • This reduces foraging time and increases foraging efficiency.
        • And the search image can contribute to frequency-dependent selection.

      • positive frequency-dependent selection - phenotype fitness increases as it becomes more abundant
        • all Heliconiid butterflies are toxic
        • different species that live in the same area have the same color patterns
        • the more common the color pattern, the more likely a bird predator will catch a toxic butterfly and quickly learn to avoid that color pattern.
        • This type of copy-cat scenario is Mullerian Mimicry

      • negative frequency-dependent selection - phenotype fitness decreases as it becomes more abundant
        • Monarch butterflies are toxic and distasteful.
        • Viceroy butterflies are non-toxic and tasty. If you're a bird.
        • Both butterfly species have the same color pattern.
        • When Viceroys are common, it will take a bird longer to learn to avoid that pattern. (Bird will catch tasty butterflies more often.)
        • When Viceroys are rare, a bird will usually catch a Monarch more quickly, and learn to avoid that pattern. (Bird is more likely catch distasteful butterflies early.)
        • The orange and black coloration is more adaptive for Viceroys when Monarchs are relatively abundant.
        • A harmless mimic copying a toxic model is known as Batesian Mimicry

    As selective pressures change with phenotypic frequency, so does the relative fitness of each phenotype.

    The Neutral Theory of Molecular Evolution

    Most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral.

    Motoo Kimura proposed that much (if not most) genetic variation across genomes was neutral (neither adaptive nor maladaptive).

    Neutral Mutations
    Not all mutations change the adaptiveness of an allele, or even change amino acid sequence.

    • silent (sort of = synonymous) mutation
      • does not change the amino acid sequence encoded by a particular gene.

    • neutral mutation
      • has little or no phenotypic effect
        or
      • has no effect on the Darwinian fitness of the individual carrying it

    A neutral mutation is neither adaptive nor deleterious, but it should not be confused with a silent mutation. The distinction is subtle, but important.

    Is a silent mutation always neutral? Not necessarily. (<--required link)

    • change to a triplet matching a more common or more rare tRNA can cause an upregulation or downregulation of the rate of production of the gene's product.

    • change to a more rare triplet can cause a change in final protein configuration

    Pseudogenes vs. Protein-coding Genes
    The proteome is the entire complement of proteins that is or can be expressed by a cell, tissue, or organism.
    But the genome contains more than the proteome genes.
    There are also:

    • genes that code for functional RNAs not translated into protein
    • non-coding functional DNA (e.g., the ends of chromosomes)
    • non-coding pseudogenes: genes that no longer appear to have any function

    If the neutral mutation model is true, then one should predict that there will be more neutral mutations found in pseudogenes than in proteome (or RNA) genes, simply because mutations in the pseudogenes do not matter. Mutations in the proteome or RNA genes, however, might have phenotypic consequences, and be subject to natural selection.

    It turns out to be true: pseudogenes DO carry more mutations than proteome genes.


    The Molecular Clock

    The molecular clock hypothesis was originally proposed by Emile Zuckerkandl and Linus Pauling in 1962.

    It gained wider traction when Kimura proposed his Theory of Neutral Evolution in 1968.

    In a nutshell...

    • Random mutations should occur at a relatively constant rate
    • Thus, neutral mutations should become fixed in populations at a relatively constant rate
    • The degree of mutational change in a particular gene shared by several taxa should serve as an index of how long ago the lineages diverged from a common ancestor.

    For example, the number of mutations in a mitochondrial cytochrome c gene is proportional to how long ago two compared taxa split from a common ancestor:

    Neutral mutations do accumulate at a roughly regular rate. But...

    • neutral evolution is different in different organismal lineages
    • different genes evolve at different rates
    • the rate of neutral evolution can speed up or slow down over evolutionary time for any given gene
    For this reason, the study of neutral evolution employs statistics to examine the probability that a given evolutionary change is associated with a particular time frame.

    The use of the molecular clock is not without controversy within the scientific community. But if it is carefully and meticulously applied, it can yield important information. Let's explore the Molecular Clock.


    Both Natural Selection and Neutral Evolution contribute to the variety we see today, but the degree to which each contributes depends on the organism, the selective environment, and many other factors.