CH3: Evolution by Natural Selection

Chapter 3: Evolution by Natural Selection

I. Core Principles of Evolution by Natural Selection

A. Conditions for Natural Selection

Natural Selection is a process driven by three fundamental conditions:

Variation: Individuals within a population exhibit differences in their traits. These variations are the raw material upon which selection acts.
- Example: Beetles in a population display varying shades of red, from dull to bright.
Inheritance: Offspring tend to resemble their parents, meaning these varying traits are passed down from one generation to the next. This ensures that advantageous traits can accumulate in a population.
- Example: Brighter colored beetles tend to have brighter colored offspring.
Differential Reproductive Success: Individuals with certain traits are more successful at surviving and reproducing in their environment compared to others. This leads to a higher representation of these advantageous traits in the next generation.
- Example: Brighter (redder) beetles are bitter, and predators learn to avoid them. Consequently, these brighter beetles are more likely to survive, reproduce, and pass on their bright coloration compared to dull-colored ones.

B. Result of Natural Selection

When these three conditions are met, the proportion of different variant traits within the population changes over time. This change in trait frequency across generations is evolution by natural selection.

C. Semantics of Natural Selection

Fitness: This refers to an individual's ability to survive and reproduce successfully within its specific environment. It's about passing on genes to the next generation.
Adaptation: An adaptation is a specific trait or characteristic of an organism that increases its fitness relative to individuals lacking that trait. Adaptations are the products of natural selection.

II. Four Key Points in Understanding Natural Selection

Mutations Generate Variation:
- Mutations are one of the primary sources of new genetic variation upon which natural selection can act.
- Crucially, mutations occur randomly with respect to the needs of the organism. This means a mutation arises independently of whether it would be beneficial or detrimental, and natural selection then acts on the existing variation.
- While some mutations might be favored by natural selection, their occurrence is not directed by selective pressure.
Traits are the Object of Explanation:
- When studying natural selection, the focus is on how a particular trait (or characteristic) changes or remains constant over time within a population.
- Traits can be diverse:
  - Physical traits: e.g., feather color, body size.
  - Behavioral traits: e.g., bold-shy foraging tendencies.
  - Genetic traits: specific genes or alleles.
  - Physiological traits: e.g., metabolic rates, disease resistance.
Populations Change Over Time (Not Individuals):
- Natural selection is a process that operates at the population level; it changes the traits of populations, not individual organisms.
- While selection acts on individuals (e.g., an individual with a beneficial trait survives and reproduces more), the outcome of natural selection is observed as a shift in the distribution of traits within the population across generations.
- Therefore, studying natural selection requires focusing on specific populations and their dynamics.
Genotype Interacts with Environment to Produce Phenotype (GxE):
- Natural selection does not directly act on genotypic differences but rather on phenotypic differences (the observable traits).
- Understanding the interplay between an organism's genotype (G) and its environment (E) is crucial because it shapes the phenotype.
- A gene does not solely code for a trait; rather, it codes for how a trait manifests within a specific set of environmental conditions.
- Example: Plant Height and Elevation
  - The height of a plant often depends on an interaction between its genotype and the altitude at which it grows.
  - If identical seeds (same genotypes) from a plant population are grown at three different altitudes (high, medium, low):
    - Genotype 1 might grow tall at high and low elevations but short at medium elevations.
    - Genotype 4, in contrast, might exhibit an opposite response pattern to elevation changes.
- This GxE interaction often leads to the production of a reaction norm, which describes the range of phenotypes that a single genotype can express across different environmental conditions.
- Reaction norms help us understand an organism's flexibility or sensitivity to environmental changes.

III. Model Systems for Studying Natural Selection

Scientists use various model systems to study natural selection, including:

Darwin's Finches
Oldfield mouse
Trinidadian guppies
Sticklebacks
Drosophila (fruit flies)
E. coli (bacteria)

IV. Case Study: Evolution of Coat Color in Oldfield Mice

This system demonstrates the conditions for natural selection in a real-world context.

A. Background

Environment: Oldfield mouse populations face significant mortality from visually hunting predators (e.g., owls).
Variation in Habitats: Most of the mouse's range features dark coloration (inland, vegetated environments), but on Santa Rosa (Florida) beaches, mice have much lighter coat colors (coastal dunes, light sand).
Hypothesis: Natural selection favors a match between coat color and the environmental background.

B. Predictions

Light coat color will be favored in coastal dune populations living on light sand.
Dark coat color will be favored in inland populations living in more vegetated environments.

C. Testing the Conditions for Natural Selection

Is the population variable?
- Observation: Yes, coat color varies both across different populations (e.g., between beach mouse subspecies like Perdido Key, Santa Rosa Island, Choctawhatchee, etc., and the Oldfield mouse) and within individual populations. The slide shows shading representing the proportion of individuals with different pigmentation, darker shading meaning darker pigmentation.
Is some of the variation heritable?
- Observation: Yes, coat color is a heritable trait.
- Heritability Estimate: It has a high heritability (h^2 = 0.7-0.9).
- Genetic Basis: Molecular studies (Steiner et al., 2007) identified two major pigmentation genes responsible for pale coat coloration compared to dark mainland coats:
  - Melanocortin-1 (Mc1r) receptor
  - Agouti signaling protein (Agouti)
- A single amino acid mutation in these genes, or an interaction between them, creates the different colors (identified via Quantitative Trait Loci (QTL) studies).
Is there differential survival?
- Experimental Setup: Pairs of light and dark colored silicone mouse models were placed in different environments (light background/beach and dark background/inland) for 25 minutes.
- Measure: The percentage of models attacked by predators was recorded. If neither was eaten, a score of 0\% was given.
- Results:
  - Light background (beach environment): Predators attacked dark models significantly more (Approx. 85\% attacks) than light models (Approx. 15\% attacks). This indicates light coloration offers a survival advantage in light environments.
  - Dark background (inland environment): Predators attacked light models significantly more (Approx. 80\% attacks) than dark models (Approx. 20\% attacks). This indicates dark coloration offers a survival advantage in dark environments.
Did the population evolve (i.e., did fitness vary)?
- Experimental Setup: Semi-natural enclosures (50 \text{ m} \times 50 \text{ m}) were built in sand dunes (light site, where deer mice are normally light) and in dark vegetation (dark site).
- The probability of survival was examined as a function of dorsal fur coloration in these enclosures.
- Results:
  - Light site: Mice with lighter dorsal fur brightness had a significantly higher probability of survival.
  - Dark site: Mice with darker dorsal fur brightness had a significantly higher probability of survival.
- Conclusion: Natural selection operates very strongly in both experimental populations, favoring camouflage that matches the background. This demonstrates evolution occurring in response to selective pressures.

V. Case Study: Trinidadian Guppies

This system illustrates how predation pressure drives the evolution of life history traits.

A. Environmental Differences

Low-predation sites: Typically feature only the Rivulus hartii predator (which primarily preys on smaller, immature guppies).
- Guppies in these sites tend to produce fewer but larger offspring.
High-predation sites: Feature predators like Crenicichla alta (which preys on larger, adult guppies).
- Guppies in these sites tend to produce many small offspring.

B. Life History Trait Differences

Guppies from low-predation sites average larger offspring size and fewer offspring.
Guppies from high-predation sites average smaller offspring size and more offspring.

C. Transplant Experiment: High to Low Predation

Experiment: Guppies from a high-predation site were transferred to a previously guppy-free low-predation site.
Prediction: Over generations, the transplanted guppy population would evolve life history traits similar to the native low-predation guppies.
Outcome: The guppies evolved to produce fewer, larger offspring, demonstrating natural selection acting rapidly on life history traits in response to a change in environmental conditions (specifically, reduced predation).

VI. Case Study: Natural Selection in the Lab (E. coli Long-Term Evolution Experiment)

This system demonstrates directed evolution in a controlled laboratory setting.

A. Experimental Setup (Lenski's Experiment)

Initiation: A single bacterial clone of E. coli was used to create 12 genetically identical lines.
Daily Protocol (over 15,500 days / 75,000 generations):
- Each day, cultures were grown overnight.
- A 100-fold dilution was performed daily to transfer a small portion to fresh media, creating selection for efficient growth in a specific environment.
- Periodically, samples were stored in a -80^ ext{o}\text{C} freezer to preserve ancestral and evolved strains for later comparisons.
Outcome: The evolved strains and their frozen ancestors are now available for a wide range of evolutionary studies.

B. Observed Evolutionary Changes

Cell Volume: Over time (generations), the cell volume of E. coli significantly increased, indicating an adaptation for larger cell size which might confer a competitive advantage in the given medium.
- Initial volume was around 0.4\text{ fl}, increasing to over 0.7\text{ fl} by 10,000 generations in some lines.
Relative Fitness: The relative fitness of the E. coli populations (as measured by competitive growth against the ancestor) consistently increased over generations.
- Initial relative fitness was 1.0, and it rose to approximately 1.6 in many lines by 10,000 generations, demonstrating continuous adaptation.

VII. Constraints on What Natural Selection Can Achieve

Natural selection is a powerful process, but it operates within certain limitations.

A. Short-Term Constraints: Limited Genetic Variation

The rate of adaptation in a population is often proportional to the supply of new genetic variation available for natural selection to act upon.
If there isn't suitable genetic variation for a trait to change in a beneficial direction, natural selection cannot produce that change.
Paradoxically, an influx of too many genes from a neighboring population (gene flow) can limit local adaptation.
- This occurs if the incoming genes are from a larger population facing different selective pressures, potentially swamping out locally beneficial alleles.

B. Physical Constraints

Natural selection operates on physical structures in the material world, and as such, it is constrained by the same physical laws that govern those structures (e.g., laws of physics, chemistry, biomechanics).
Example: Eye Placement (Ostrich vs. Owl)
- Ostrich: Eyes are placed on the sides of the head.
  - Advantage: Provides an almost full 360 degree field of total vision, crucial for vigilance against predators approaching from any direction.
  - Disadvantage: Affords almost no stereoscopic (binocular) vision because the fields of each eye hardly overlap (0 degrees of binocular vision).
- Owl: Eyes are set on the front of the head.
  - Advantage: Allows for full stereoscopic vision of the environment (180 degrees of binocular vision), essential for visually hunting prey with depth perception.
  - Disadvantage: Presents a much more limited total field of view compared to the ostrich (180 degrees of total vision).
- This highlights a trade-off; optimal vision for one purpose (predator vigilance) may conflict with optimal vision for another (predator hunting).

C. Overcoming Constraints

Organisms can evolve compensatory mechanisms to