BIOL 4160

Evolution

Phil Ganter

301 Harned Hall

963-5782

Pollen newly released from the maturing flowers on this spathe

03 - Genetic (and some Phenotypic) Variation

Email me

Link to a list of Specific Objectives for lectures

Back to:

Academic Page 
Tennessee State Home page 
BIOL4160 Page 
Ganter home page 

Types of Gene Variation

Structure of Genetic Material

  • What is a gene (exon, intron, control region, alternative splicing)
  • Gene, Allele, and Locus
  • Single Copy versus Repetitive DNA sequences
  • rDNA Tandem Repeats (ITS = Internal Transcribed Spacer)
  • Microsatellites short repeated sequences (microsatellites = simple sequence repeats or SSRs) - 2-8 base pairs, tandem repeats (# of repeats variable) used to map an allele
  • LINES (long interspersed repeats) up to 5000 bp in length
  • SINES (shorter than LINES)
  • Transposons, Latent Viruses
  • Gene families (based on protein families)
  • Pseudogenes                                                                                                                                                                                                                                                            

Mutations (point, substitution) and Third Codon Degeneracy

  • (Transversion, Transitions, Synonymous and Non -Synonymous, termination)
  • INDEL Mutations often mean loss or alteration of function
  • Single-Nucleotide Polymorphisms (SNP's) are useful mapping markers and can label individuals
  • Neutral mutations have no effect on the fitness of the organism
  • Synonymous nucleotide substitutions (3rd position of the codon) are neutral because there is no alteration of the phenotype
  • If a mutation alters a protein, it may do so in such a way as to not alter its function, also neutral
  • Neutrality is probably most common outcome
  • Deleterious Mutations decrease fitness
  • Pleiotropic effects - a gene that affects more than one phenotypic trait (eye color mutations of Drosophila exhibit pleiotropy)
  • Beneficial mutations occur at a low rate but this is expected in Darwin's gradualist view of evolution
  • Epistasis is when two or more loci interact in their effects on a phenotype

Gene conversion, intergenic recombination

Unequal crossing over and gene duplication

Chromosomal Variation

  • Ploidy Changes
    • Aneuploidy, Polyploidy (Allopolyploidy, Autopolyploidy)
  • Inversions
  • Translocations
  • Fission and Fusion
  • Karyotype Variation

Figure 1 - Karyotypes of 36 strains of an asexual yeast, Candida sonorensis, showing the sorts of extreme karyotype variation found with asexual "species."   It is often hard to be sure that a yeast is truly asexual but it is hard to see how synapsis during meiosis could be achieved between some of the strains of this yeast.  There are no known phenotypic differences between the strains listed below.  This raises two related questions.  First, are we missing important parts of the phenotype?  If not, where did the extra DNA in the larger genomes come from and what does it do?

Mutation, Variation, and Randomness

Variation is ultimately the outcome of mutation

Mutation is a random process

  • Thus, mutations do not happen when the will help an organism
  • Most are neutral, some are harmful, and the least likely outcome is a mutation that is helpful
  • Recent challenges to this assertion have been shown to be wrong and have reinforced the assumption of randomness in mutations

Mutation rate is not a random effect

  • Different lineages have different rates of synonymous mutation

Although mutations are random, variation is the outcome of many mutations and is predictable!

Natural selection, in cases where there is a single allele or combination of alleles, genetic drift, and inbreeding will work to reduce variation in a population, which can only be replenished by migration of new alleles or mutation

Problem:  When lab populations of animals are subject to artificial selection, the most common response it that the character being selected changes in the direction encouraged by selection.  So, one can reduce the number of facets (individual visual cells) in the eye of a Drosophila by selecting for this by only allowing flies with the fewest facets to contribute eggs to the next generation.  Wim Scharloo did a laboratory selection experiment with a population of 1000 flies.  After several generations of selection during which the character selected changed, change stopped.  Prof. Scharloo then made one change in the experiment.  He increased the population size from 1,000 to 10,000.  Selection almost immediately became effective again and the character continued to change.  Why did the expansion of the population restart the evolutionary process?

Recombination and Variation

Parasexual recombination (conjugation, transduction, transformation)

  • Horizontal versus Vertical Transmission
  • Recombination at the molecular level
  • Homologous and Non-homologous

Sexual recombination

  • combinations of genes are not preserved unless the genes are closely linked (no linkage is ever tight enough to completely prevent recombination)
  • Recombination can be intergenic
  • Recombination produces new combinations of genes each generation
  • To preserve favorable combination of genes, some other process must operate (positive assortative mating is one possibility)

Linkage

  • Physical linkage means that the loci are close enough on a chromosome that they are likely to be inherited together
  • If two loci each have two alleles in a population and the proportion of each allele is 0.50, then unlinked genes should be in Linkage Equilibrium
    • in this case, 25% AB, 25% Ab, 25% aB, and 25% ab,
  • Linkage Disequilibrium is a significant departure from the proportions expected from linkage equilibrium
    • In the case above, if Ab is one chromosomal type in the population and aB is the other (and no recombination occurs because the linkage is so tight) you get 50% Ab, and 50% aB (no recombinant allele parings [AB or ab] are formed)
    • Linkage disequilibrium, then, is a measure of the inhibition of recombination and indicates some evolutionary process may be affecting the outcome of recombination (assortative mating, selection, etc.) in addition to simple physical linkage

Hitchhiking - when one allele is changing frequencies due to selection (for or against), neighboring alleles may also change if closely linked

Hardy-Weinberg

Variation is a population-level phenomenon (emergent property of populations) and a necessary condition for evolution

What should we expect to happen over time when variation exists in a population?

Hardy-Weinberg expectations are predictions of future population variation when that variation is not altered by ecological or statistical processes

p2 + 2pq + q2

H-W Assumptions - Hardy-Weinberg predicts no change but is only accurate if its 5 assumptions are met.  Below we list the assumptions and discuss what happens when the assumption is violated.

No mutation,

Mutations generate differences between generations and upset H-W prediction

No migration,

If populations differ in their genetic composition (maybe A is 90% of the genes at a locus in one population and only 10% in another population), migration between the populations can change their genetic composition

Random Mating,

Assortative mating (also called Non-Random Mating)

  • Positive Assortative Mating - if like mates with like (due to choice or to small population sized not allowing much choice) then intermediates and heterozygotes are lost - a decrease in genetic variation
  • Negative Assortative Mating - like mating with unlike will increase the proportion of heterozygous intervals and preserve genetic variation

Inbreeding

  • has the same effect as positive assortative mating - loss of genetic variation
    • two related individuals are more likely to have a rare allele, given that one of them does, than two individuals chosen at random from the entire population, thus rare recessive alleles are more likely to become homozygous in inbred offspring
  • can (not must, but can) lead to lower viability of inbred individuals or to lower fecundity
    • Heterosis - condition where the heterozygous individuals show greater fitness (viability, fecundity) than do individuals homozygous for either of the alleles
    • Inbreeding Depression - loss of fitness due to inbreeding as more and more recessive, less fit alleles are expressed due to inbreeding
  • more likely in small populations
  • often there are physical or behavioral barriers to inbreeding

Large Populations,

Genetic Drift

  • loss of genetic variation due to chance events
  • more likely in small populations than in large
    • Neighborhoods can enhance the effect of drift
    • if populations are subdivided into small neighborhoods, then drift will be more important for the entire population
  • Bottleneck - a sudden low point in populations numbers, followed by expansion of the population
    • Bottlenecks can reduce genetic variation in a generation through genetic drift, even though population numbers are generally high
    • If you come along when the population has recovered its large size, you would think that genetic drift was not important in that population, but a recent bottleneck event might have greatly reduced genetic variation in your study population.

    Founder Effect

    • if new populations are formed by the migration of just a very few individuals, the population can be said to have gone through a bottleneck at its founding
    • founder effect can mean that new populations are different from parent populations through chance alone
  • No Selection

    Natural selection is the outcome of fitness differences between individuals

    • Natural selection requires that there is heritable genetic variation in a population
    • if some of those genetic variants are more fit (better able to survive and reproduce) than others, the fit genetic variants will leave more offspring that also have their "fit" genotypes
    • as time goes on, more of the population are descended from the more fit individuals
      • An example - Peppered Moth melanic forms favored when trees are darkened, light form when trees are lighter
        • selective factor is mortality due to bird predation
        • melanic gene has other effects, but none are strong enough to explain the population changes seen in England
        • in the US, melanic form has declined even though trees are not becoming lichen covered, so NS by bird predation may not work for all cases of Industrial Melanism
      • Prevalence of resistance to herbicides, insecticides, rat poisons, and antibiotics are also examples of natural selection

    Natural Selection can enhance, reduce, or maintain variability

    • Natural selection can, under the right conditions, favor polymorphism (two or more alleles or phenotypes in a population) can result in a Balanced Polymorphism if each phenotype has an environment in which it is most fit form
      • Cepaea snail's (a large land snail) shell banding varies with the background and can hide the snail from bird predation
      • populations are made up of different forms, each form with an environment in which it is the fittest
      • natural selection favors more than one phenotype within a single population here
    • Natural selection can have different effects on a population, which we have divided into three "modes of selection."
      • Disruptive (Diversifying)
        • when the extremes are fittest and intermediates are less fit
        • Can split a population into two phenotypes with few intermediate forms
      • Stabilizing
        • when the fittest individuals are the average, then those with more extreme (larger and smaller) phenotypes are less fit and NS will act to reduce the number of individuals with extreme phenotypes
      • Directional
        • when a new, fitter type originates, the population will move from the older type to the newer type over time

    Natural Selection produces Adaptations

    • Adaptations are those characteristics of organisms that allow one organisms to be more fit than another
    • Populations adapt to environments as natural selection increases the proportion of individuals that have the most fit adaptation
    • All three modes of selection (disruptive, directional, and stabilizing) will produce adaptation (in the case of disruptive, more than one adaptation).

Variation Within Populations

Are all differences among individuals in a population heritable genetic variation?

Phenotypic Variation (Vp) = Environmental (VE) + Genetic (VG)

Genes may have different effects when in different environments

  • many genes are expressed differently when temperature differs
  • expression of many genes depends on genetic environment - what alleles are present at other loci - dominance is a good example of this effect
  • Therefore, we must added a term for gene-by-environment interactions (VG+E)

Phenotypic Variation (Vp) = Environmental (VE) + Genetic (VG) + Interaction (VG+E)

Heritability

  • Proportion of phenotypic variation that is due to genetic variation

h2 = VG  / (VG + VE)

  • Note that the interaction term is not used and, if significant, makes heritability harder to measure and discuss
  • Often estimated through the slope of the line describing the relationship between the measure of a character in offspring versus the mean of the parents (Midparent Mean)

Reaction Norms

  • A reaction norm is the change in phenotype produced by a single genotype in different environments
  • This is a way to quantify Gene x Environment interaction
  • often a scattergram with the phenotypic measure as the y-axis and the different environments (or range if the differences are continuous, like temperature differences) on the x-axis
  • each genotype gets its own line and interactions are revealed when lines are not parallel

Variation Between Populations

We have already discussed the geographic relationship among populations (allopatry, peripatry, parapatry - no sympatry for populations of the same species!!) when discussing speciation

  • Subspecies = Geographic Race
  • Clines form between extremes of populations or between parapatric populations

Adaptive Geographic Variation and Gene Flow

  1. AGV adapts a local population to its specific, local habitat
  2. Gene Flow counteracts AGV by homogenizing gene frequencies in a population or between local populations

Countergradient Variation

  • a plant found in both harsh and benign environment grows slowly in harsh environment and quickly in benign environment
  • experiment - grow seeds from both populations in the benign environment
    • seeds from population in harsh environment grown faster than seeds from population in the benign environment
    • Environmental variation causes a gradient in growth rate
    • Genetic variation produces a counter-gradient in growth rates due to natural selection for faster growing plants in harsh environment
    • But, since the environmental effect is larger, one observes that plant grown more slowly in harsh environment (difference would be even greater without the genetic countergradient)

Character Displacement

Variation among populations of a species as a result of some populations being sympatric with a related competitor species (or within populations in which gene flow is limited by distance and part of the population is sympatric and part is not)

Character is displaced (=altered) by the effect of competition with the related species for resource, not by a change in overall resource availability

(see book for examples)

F-statistics

  • Variation among individuals in a species can be subdivided into within-population and between-population components
  • FST is a measure of the proportion of variation among individuals at a locus due to differences between populations and it ranges from 0 (no difference in allele frequencies) to 1 (different alleles fixed in each population)
  • There are several ways to calculate and/or estimate this and we will examine one here based on a locus with two alleles only (in all populations)
  • To calculate this, it is necessary to know the frequency of the alleles in each population, from which you can calculate the mean (q-bar) and variation in q (VAR).

  • This equation will be 0 if there is no variation among populations (numerator = 0) and 1 when that variation is as large as the product of the average frequencies of the two alleles (1 - q is the frequency of the other allele when only two are present)
Last updated February 11, 2009