Chapter 7

Mainland mice are dark brown on top and have a small white patch limited to their underside.

The beach mice's light coat blends into the dunes' white background.

The populations diverged only recently

• with distinguishable phenotypes

• heritable phenotypes

Parents with dark coats generally produced offspring with dark coats, similarly, parents with light coats produced offspring with light coats

• therefore, this must be attributable partially to genetic variation via eggs or sperm

Variations in mouse color are not due to a single locus

• polygenic - expression is influenced by many genetic loci

• depend on non-additive interactions between alleles at those loci (epistasis)

• or they can be shaped by the interaction between alleles and the environment (phenotypic plasticity)

Phenotypic differences among individuals are usually quantitative rather than qualitative because of polygenic traits.

Quantitative genetics is the study of continuous phenotypic traits and their underlying evolutionary mechanisms

As loci (alleles) are added, the number of possible genotypes and phenotypes increases.

Variance

• the amount of variation for a trait in a population

• traits the vary widely have a larger variance than traits that are practically identical in every individual

• calculate how far each trait deviates from the mean of the population

• square each deviation and divide the sum of squares by the number of individuals in the sample

Variance in Phenotypic Trait (VP)

• the sum of several different kinds of variances

• genetic variance (VG), environmental variance (VE)

• for some traits, the environment plays a larger role than genetics (VE > VP)

• if the environment has no effect, then VP = VG

Heritability

• broad sense heritability (H²) is the proportion of the total phenotypic variance that is attributable to genetic variance

• H² = V_G/V_P = V_G/(V_G+V_E)

• however, it represents all genetic variance as a single value

• real genetic variance is more complicated

  • for example, in sexually reproducing individuals, not all of the individual’s genotype is transmitted to offspring

  • only additive alleles are passed on regardless of what it is paired with

• therefore, only some of the genetic variation actually contributes to the phenotypic resemblance between offspring and parents

  • only this portion enables a population to evolve in response to selection

Why narrow sense heritability (h²) doesn’t include Dominance or Epistasis

• in additive alleles, they influence the phenotype the same way regardless of what the other allele would be

  • act independently of each other

• dominance results from when interactions occur among alleles with sister alleles on the other chromosome

• epistasis occurs when an allele interacts with alleles at other loci elsewhere in the genome

• in both dominance and epistasis, the allelic effect of the phenotype depends on what the other allele is

• their effects disappear each generation

For bacteria (do not undergo meiosis) and inbred populations, broad sense heritability is a good measure

• inbred populations - so many of the alleles are homozygous

• bacteria - epistasis interactions have an important effect

V_G = V_A + V_D + V_I

V_A is what causes a population to evolve predictably in its phenotypic distribution following selection

h² = V_A/V_P

Estimating narrow sense heritability:

• randomly pair individuals together, breed them, and measure the trait in parents and offspring

• the greater the heritability, the more similar offspring should be to their parents

• a greater response (R) results from a higher narrow sense heritability

Directional Selection - selection can shape populations by favoring individuals with trait values at one end of a distribution

Stabilizing Selection - selection can shape populations by favoring individuals with trait values near the middle of a distribution

Disruptive Selection - selection can shape populations by favoring both ends of a distribution

Selection and evolution are not the same

• populations can experience selection even if they cannot evolve in response to it

• selection can potentially lead to evolution if the difference in reproductive success is tied to genetic variation

• depends on the amount of variation and if the variation is heritable

Evolutionary Response (R) is the product of the strength of selection (S) and the extent to which offspring resemble their parents for that trait (h²)

Selection Differential (S) difference in mean of the trait of reproducing individuals to the mean of the trait for the general population

Linkage Equilibrium - because of independent assortment, alleles for loci on different chromosomes are predicted to be inherited independently from each other

• any two loci located on different chromosomes have only a 50% chance of being packaged together in the same gamete

• chances of maternal and paternal alleles being inherited together are random

• P_A1A2 = P_A1 x P_A2

Because of genetic recombination, alleles at loci on the same chromosome may be mixed and matched to the point that they also assort independently if they are located far enough apart that recombination occurs

Linkage Disequilibrium - when loci are located closer together, however, the probability of recombination decreases

• if chromosomes were passed down unchanged like beads on a string then their state would be the opposite of linkage equilibrium

• certain alleles inherited together more often

• results from loci being physically adjacent (it takes many generations for meiosis to uncouple loci that are located very close to each other on a chromosome)

• P_A1A2 ≠ P_A1 x P_A2

• To find the extent of linkage disequilibrium, it is observed frequency - expected frequency

Loci located far apart on the chromosome have a high probability of being swapped by recombination

During a new mutation event and a hybridization event, linkage disequilibrium exists at first all the way along the entire chromosome

• When a new mutation arises, it first appears on a single chromosome.

• This means the new allele is initially linked to the alleles already present at nearby loci.

• Over generations, recombination will break this association, but at first, the new allele remains in LD with its original chromosome neighbors.

• When two genetically distinct populations interbreed (hybridize), their alleles are initially in strong LD because the two populations had different genetic backgrounds.

• This means some allele combinations are much more common than expected by random chance (because they came from the original populations).

• Over time, recombination breaks these associations, but in early hybrid generations, LD is high.

Sometimes, selection can vary certain combinations of alleles

• works opposing recombination

• increases the physical linkage and reduces the rate of recombination

• supergenes are close enough to each other that they function as one unit

Yellow monkeyflower

• inhabits a wide range of environments

• inland populations adapt to dry soils and hot summer conditions

  • annual plants: to escape the heat, they plant flowers early in the year (before summer) and die after flowering

  • their seeds remain buried in the soil until it rains the following year

• on the coast, populations wait longer before flowering because of the cooler, moister environment

  • perennials: they survive all year round and flowering later in the summer to allocate more resources for growth early in the year

• mixing and matching inland and coastal alleles for different traits would be disastrous

• the genes for these traits were located very close on the chromosome (formed a supergene)

  • inverted for coastal populations

Quantitative Trait Locus (QTL)

• stretch of DNA correlated with variation in a phenotypic trait

• example, with fish

  • inbreed large fish and inbreed small fish to become homozygous

  • take a female homozygous from one line and mate it with the male homozygous from another line

  • F₁ is the first generation of offspring (heterozygous)

  • F₂ is the second-generation offspring (when heterozygotes mate with each other)

  • the F₂ population has a wide range of body sizes because genetic recombination swapped pieces of the chromosome from each of the original parental types

  • some fish will carry a high number of large alleles, while others inherited more of the small allele

  • by examining the DNA of F₂ fishes, you can correlate to see whether each marker came from large-body-size copy or small-body-size copy

• For mice, Agouti and Mc1r produce proteins that are critical for synthesizing dark pigments

  • the lighter coat on beach mice resulted from a mutation that changes a single amino acid in Mc1r (decreases the effect of the receptor) and a second mutation increases the expression of Agouti

  • high expression of Mc1r results in dark pigment

  • Agouti causes the light pigment by encoding a repressor that shuts down the Mc1r receptor

    • it delays the maturation of melanocytes

    • beach mice have a stronger expression of Agouti on their dorsal than mainland mice

Genome-Wide Association Mapping (GWA)

• require detailed maps of the entire genome of species and genotype information for a very large number of individuals

• very effective for humans

• begins with large numbers of individuals → grouped according to phenotype → compared marker for marker across the entire genome to identify alleles for the trait of interest

QTL and GWA mapping studies help identify regions of the genome responsible for genetic variation in phenotypic traits.

• to identify the genes responsible for phenotypic evolution

Organisms may differ in how they react to environmental situations, and these differences can be heritable

• phenotypic plasticity - when responses to environmental differences evolve

Traits that are shaped by responses to the environment are known as plastic.

• a plant growing in low light will grow larger leaves to capture more light compared to one that grows in direct sunlight

  • but the biomass will be lower as they maximize energy to grow leaves

Snowshoe hairs have brown fur during the summer but as they sense autumn, they molt and grow a coat of white fur to match the snow

• avoid being killed by predators

Reaction norm diagram is used to visualize the responses of organisms to the environment

If V_G×E is significant, it means some genotypes perform better in certain environments, while others perform better in different environments.

• plastic responses of organisms to their environment can evolve