AP Bio unit seven evolution Notes

Artificial Selection

• Also known as selective breeding.
• Breeders select organisms with desired traits over many generations.
• Creates a gene pool with individuals having genes for the desired trait.

Examples

• Brassica oleraceae family: Cauliflower (flower clusters), Broccoli (flower buds), Brussels sprouts (lateral buds), Kale (leaves) - all bred for specific traits.
• Dogs: Bred from wolves (Canus lupus) for specific purposes like protection, hunting, or companionship, resulting in various breeds.

Natural Selection

• Variation: Exists within any population; inherited variation in genes through recombination and mutation.
• Reproduction Rate: Number of individuals born exceeds the survival rate.
• Survival: Survivors possess a beneficial trait providing an advantage.
• Adaptation: Mutation continues to create new variants, leading to adaptation over generations.

Examples of Adaptations

• Wing structure of a bat.
• Behavioral adaptation like sonar in bats.
• Camouflage mutations like in the satanic leaf gecko.
• Molecular level adaptations like enzyme-substrate fit.

Sexual Selection

• Selection for traits increasing reproductive success.
• Results in sexual dimorphism (different phenotypes in males and females).

Types of Sexual Selection

• Intersexual Selection: Members of one sex choose mates based on traits of the other sex (e.g., female turkeys choosing attractive males based on tail feathers and behavior).
• Intrasexual Selection: Competition between males for access to females or breeding territories (e.g., elephant seals, where larger, aggressive males control harems).

Phenotype Distribution

• Population characteristics often follow a bell curve with continuous variation.

Types of Selection that Alter Phenotype Distribution

• Directional Selection: Selects against one extreme, shifting the population towards the other extreme.
• Stabilizing Selection: Selects against both extremes, favoring the average phenotype (e.g., birth weight in babies).
• Disruptive Selection: Selects for both extremes, potentially splitting the population into two groups.

Adaptive Melanism

• Darkening of the body in a population due to environmental changes.
• Genes for lighter coloration are selected against, while genes for darker coloration are selected for.
• Selective pressure is typically predation.

Example

• Rock pocket mouse evolving darker coloration on dark substrates due to a mutation increasing melanin production.

Evolutionary Fitness

• Measured by the number of offspring and offspring's offspring that survive to reproduce.
• Fitness is relevant at every stage of the life cycle enabling genes to be passed to the next generation.

Peppered Moth

• Demonstrates directional selection and adaptive melanism in response to environmental change.
• Before the Industrial Revolution:
  • Predominant phenotype was peppered (light).
  • Moths were camouflaged on light-colored tree trunks.
• During the Industrial Revolution:
  • Soot darkened tree trunks.
  • Dark-colored moths had a selective advantage.
  • Population shifted from light to dark moths.
• After Clean Air Act:
  • Pollution declined, lichens returned, trunks became lighter.
  • Mean phenotype shifted back to light-colored moths.
• Observed and replicated case of adaptive melanism.

Population Genetics

• Study of how genes are distributed in populations and how they change over time.
• Allele Frequency: Key measurement; example given of a population where the frequency of allele 'a' is 0.5.
• Gene Pool: All alleles of all genes in a population.
• Evolution Change in the genetic makeup of a population over time; change of allele frequencies within a gene pool.
• Dominant allele does not have to be more common than the recessive allele; allele frequency is based on advantage/harm or random historical factors.
• Achondroplasia is an example of a rare dominant allele.

Hardy-Weinberg Equations

• p + q = 1
• p^2 + 2pq + q^2 = 1

Variables

• p = frequency of the dominant allele.
• q = frequency of the recessive allele.
• p^2 = frequency of homozygous dominance.
• 2pq = frequency of heterozygotes.
• q^2 = frequency of recessive individuals.

Sample Problem

• 49% of mice have white fur (recessive trait).
• q^2 = 0.49
• q = \sqrt{0.49} = 0.7
• p = 1 - q = 0.3
• 2pq = 2 * 0.3 * 0.7 = 0.42
• p^2 = (0.3)^2 = 0.09

Hardy-Weinberg Principle

• Allele frequencies in a gene pool stay constant unless the following conditions are not met.

Conditions

• Infinitely large population.
• No harmful or beneficial alleles.
• Random mating.
• No emigration or immigration.
• No net mutation.

Factors That Cause Evolution

• Small populations (genetic drift).
• Natural selection.
• Sexual selection.
• Gene flow.
• Directional mutation.

Genetic Drift

• Random change in allele frequencies, usually in small populations.

Population Bottleneck

• Biotic or abiotic factor wipes out a large percentage of individuals.
• Survivors' alleles might not represent the original population's frequencies.
• Example cheetahs (genetically uniform due to a past bottleneck event).
• Survivors don't necessarily have an advantage (it is just luck).

Founder Effect

• A small number of individuals found a new population.
• Allele frequencies of founders may differ from the parent population.
• Results in loss of alleles.

Gene Flow

• Movement of alleles from one population to another.
• Can occur through movement of individuals or gametes.
• Changes allele frequencies, especially in the recipient population.
• Diminishes differences between adjacent populations.

Mutation

• Ultimate source of genetic variation.
• If directional, can change allele frequencies.

Population Genetics Example: Sickle Cell Disease

• Caused by a recessive allele in the gene for hemoglobin.
• High frequency in certain populations due to heterozygote advantage.

Heterozygote Advantage

• Big S Big S (homozygous dominant) is selected against due to malaria.
• Big S little s (heterozygote) is selected for (protection against malaria, no sickle cell symptoms).
• little s little s (homozygous recessive) is selected against because you have sickle cell disease.
• Correlation between the frequency of the little s allele and malaria intensity in Africa.
• Similar heterozygote advantage may apply to cystic fibrosis and Tay Sachs.

Evidence of Evolution

• Homologous Traits: Share a common underlying structure and embryological origin, showing descent with modification from a common ancestor.

Example

• Forelimbs of humans, dogs, birds, and whales have the same bones.

Adaptive Radiation

• One parent species produces several descendants with unique adaptations filling different ecological niches (e.g., Galapagos finches).

Vestigial Structures

• No apparent function but inherited from an ancestor where the structure had a function (e.g., whale pelvis, human coccyx).

Homology vs. Analogy

• Analogous Features: Similar function, different underlying structure, arise through convergent evolution (e.g., hydrodynamic form of sharks, ichthyosaurs, and dolphins).
• Wings of Birds and Bats: Analogous for flight, but forelimbs are homologous.

Molecular Homologies

• Molecules with similar structure and monomer sequence indicating common ancestry (e.g., hemoglobin in vertebrates).

Example

• Differences in amino acid sequence of hemoglobin between different species relative to humans (gorilla > rhesus monkey > mice > chickens > frogs).

Pseudogenes

• Nonfunctional genes that are variants of functional genes in related species (e.g., GLO pseudogene in humans and primates).

Origin and Loss

• Shared ancestor in rodents, primates, bats, and guinea pigs contained the GLO gene and could able to produce Vitamin C.
• Mutation broke the gene (GLO Pseudogene).
• These pseudogenes are convergent features and are analogous not homologous.

Universal Homologies

• DNA as genetic material.
• ATP for energy coupling.
• Same genetic code.
• Ribosomes for protein synthesis.
• Shared metabolic pathways (glycolysis, Krebs cycle, ETC, chemiosmosis).

Eukaryotic Homologies

• Nucleus.
• Mitochondria.
• Endomembrane system.
• Genes with introns.
• Linear chromosomes.
• Sexual reproduction.

Embryological Development

• Early vertebrate embryos look similar; differentiation leads to adult body forms.
• Vestigial features in embryos (tail in human embryos, pharyngeal gill slits) indicate common ancestry.

Shared Development Genes

• Genes controlling development are shared among diverse species.
• Eyeless Gene: master switch for eye development in arthropods and vertebrates; can be transplanted between species to induce eye development.
• Homeotic Genes: Control body plan.

Biogeography

• Study of geographic distribution of species and varieties.
• Distribution patterns reflect evolution in one area followed by spread to adjacent areas.

Marsupials

• Mostly limited to Australia.
• Parallel evolution occurs due to niches filled by marsupials in Australia that are filled by placental mammals elsewhere.

Fossils

• Petrified remains of living things that demonstrate change over time.
• Transitional forms show descent with modification.

Dating Methods

• Relative Dating: Based on superposition (younger material on top of older layers).
• Absolute Dating: Based on the decay of radioactive isotopes (half-life).
  • Carbon-14 decays to nitrogen-14 (half-life = 5,730 years).

Observed Evolution

• Evolution of resistance to DDT in mosquitoes (and other resistance examples).

DDT Resistance

• Mosquitoes with inborn resistance survive initial DDT use and pass on genes for resistance.

Biological Species Concept

• Defines a species as a group of organisms that can naturally interbreed to produce viable, fertile offspring and are reproductively isolated from other such groups.

Limitations

• Hybridization in closely related species.
• Extinct or asexual species.
• Prokaryotic species.

Reproductive Isolating Mechanisms

• Processes, behaviors, or other traits that keep the gene pools of closely related species separate.

Prezygotic Isolating Mechanisms

• Prevent mating:
  • Behavioral: Different mating rituals.
  • Temporal: Breed during different times.
  • Mechanical: Structural barriers.
  • Habitat: Different habitats.
  • Gametic: Molecular mismatch preventing fertilization.

Postzygotic Isolating Mechanisms

• After zygote formation:
  • Hybrid Inviability: Hybrids don't develop.
  • Hybrid Sterility: Hybrids are healthy but sterile (e.g., mules).
  • Hybrid Breakdown: Hybrids can reproduce and healthy but F2 generation is weak or sterile.

Allopatric vs. Sympatric Speciation

Allopatric Speciation

• Geographic barrier leads to genetic differentiation and reproductive isolation.

Sympatric Speciation

• Occurs without geographic barrier; can occur through polyploidy in plants or adaptation to microhabitats or sexual selection in animals.

Adaptive Radiation

• One parent species produces several descendant species with unique adaptations filling different ecological niches (e.g., Galapagos finches).
• Phylogeny reflects adaptive radiation.
• Homologous and vestigial traits result from adaptive radiation.

Importance of Phenotypic Variation

• Essential for evolution; the raw material upon which natural selection acts.
• Natural selection acts on the phenotype, not the genotype.
• No variation= no adaptation or selection, which can lead to extinction.

Examples

• Phospholipid Structure: In cold climates, mammals exhibit an increase of saturated phospholipid tails in the body core and an increase of unsaturated phospholipid tails in the extremities for membrane fluidity.
• Hemoglobin: Fetal hemoglobin has a higher affinity for oxygen and contains two alpha chains and two gamma chains, adult hemoglobin contains two alpha chains and two beta chains.
• Chlorophyll: Chlorophyll A and B have slightly different light absorption properties, so plants with both can better adapt to different environments.

Extinction

• Normal part of life; most species that have ever lived are extinct.

Extinction Vortex

• Small population size, genetic drift, loss of genetic diversity, reduced fitness.

Mass Extinction

• Widespread, rapid decrease in Earth's biodiversity.
• Often caused by geological or astronomical events.

Impact on Evolution

• Leaves vacant ecological niches that promotes adaptive radiation of surviving species (e.g., diversification of placental mammals after Cretaceous extinction).
• Humans: the 6th extension are causing great loss of biodiversity due to over harvesting, destruction and fragmentation of habitats, and invasive species.

Phylogeny

• Evolutionary history also known as a phylogenetic tree.
• Built using morphological, molecular, or genetic evidence.
• Phylogenetic tree is a claim of evidence, NOT fact.
  • Shows that hippos and whales are closely related (HIPPOS + WHALES) but that (WHALES + DEER) are less closely related.

Clades

• A group of organisms that consists of a common ancestor and all of that ancestor's descendants.
• Every numbered group or all members of a given group is a clade.

Shared Derived Character

• Trait that distinguishes a clade and evolved in the common ancestor of that clade.
• Example: lungs and four limbs separate from all other organisms (see group with the frogs, lizards, alligators, robins, rats, and gorillas from the salmon).

Nodes & Sister Groups

• Node is where the brand (A-E in Phylogenic Tree) meet.
• Nodes are common ancestors.
• Sister groups are the descendants that split apart from the same node such as the common cactus finch and the large ground finch.
• Sister clade can also be called Sister Species.

OutGroups

• More distantly related group of organism that helps determing evolutionary relationship.

Misconceptions

• Do not assume that vertical closeness = evolutionary closeness. (BIGGEST MISTAKE TO AVOID)
• It's all about recency and common ancestry.
• Nodes can rotate and not change any relationships.
• Think about art form: MOBILES.

Ancestral Features

• A trait that members of a clade share, but which is also shared by larger, more inclusive clades.
• Example: Claws/Nails: mammals (rats and gorillas).

Evidence Types for Phylogenic Construction

• Pre-1960s biologists looked and determined structures and relationships using Morphalogical similarities.
• Post 1960s (thanks to Watson and Crick and the discovery of DNA), nucleotide sequence in DNA/RNA or amino acid sequence in proteins has become the most accurate determiner of relationships.

Molecular clocks

• Change is caused by mutations.
• Mutation rate is constant over time.
• Calibrate change in gene/protein when species split apart (use the fossil date to help figure this out).
  • You can use that rate to determine when other species split, rate to determine when others split.
  • Example: Hemoglobin = 20 mutations every 100 years.

AP Bio Knowledge: Origin of Life

• How did life emerge naturally?
• Cell Theory? (All cell came from existing cells… so where did the first cell come from?)
• Protein Enzyme: (enzymes make complex things. How did we get complex things that life is based on absent enzymes?)

Order of Evolutionary Advancement

(1)

(2)

*Earth became stable.

(3)

*Chemistry led to biology…Monosomers came from Polymers with no enzymes.

(4)

*Combining monomers to create protocells with vesicles to store monomers.

(5)

*Self Replicating Cells (three known domains: archaea/bacteria eukarya came as a fusion of two).

Key Experiments:

• Miller Urey Experiment (1950s) Amino Acid formed in sterile and sealed apparatus but the details were incorrect (it didn't produce life, but produced amino acids from simulated environment).

Miller-Urey Apparatus steps:

(1)

*Steam to represent the ocean water.

(2)

*Chamber represents the ocean.

(3)

*Chamber for Atmosphere with hydrogen/ methane /ammonia but no oxygen (the gas giants known at the time).

(4)

*Electrodes were used to stimulate lightning.

(5)

• Condensor to have sampling but keep the containment of the sample with no contamination.

(6)

*After some running: MILLER sampled the liquid and AMINO ACIDS.

Heredity and origins of RNA:

• It is widely believed at RNA (not DNA) was the first heredity molecule because RNA can store some genetic info in viruses, RNA can act as an enzyme, can have catalytic properties in translation etc.
• The First RNA systems evolved into the self-replication RNA, followed by encapsulation, and at this point Proto-cells and natural selection made the Last Universal Common Ancestor.

LUCA

(1)

*Lipid Bi-Layer.

(2)

• Genetic Material: DNA.

(3)

*Information used to transfere: RNA.

(4)

• Ribosome creating protien.

(5)

*Membrane Channel (energy in and waist out).

(6)

*Complex Protien/Enzyme combine monomers through dehydration or break them through hydrolysis.

(7)

• ATP Synthase.