AP Biology: Overview of Evolution

Overview of Evolution

• Evolution is a central and complex topic in AP Biology.
• The course will cover natural, artificial, and sexual selection.
• Population genetics, Hardy-Weinberg equilibrium, and evidence for evolution will be covered.
• Speciation, variation, extinction, phylogeny, and the origin of life will also be examined.

Natural, Artificial, and Sexual Selection

• Natural selection is a key concept, developed by Charles Darwin, explaining change through time.
• Artificial selection, or selective breeding, serves as the foundation for understanding natural selection.

Artificial Selection

• Breeders select organisms with desired traits over generations.
• This process creates a gene pool with individuals having genes for the desired trait.
• Plants in the Brassica oleracea family (cauliflower, broccoli, Brussels sprouts, kale) are examples.
• These plants are bred for specific traits like flower clusters (cauliflower), buds (broccoli), or leaves (kale) from the same ancestral species.
• Dog breeds, all from the species Canis lupus, are bred for specific purposes like protection or companionship.

Natural Selection

• Variation exists within any population.
• Inherited variation comes from genes through recombination and mutation.
• Reproduction rates exceed survival rates, leading to competition ("many are born, few survive").
• Survivors possess advantageous traits.
• Mutation creates new variants, leading to adaptation over generations.
• Adaptations can be structural (bat wings), behavioral (bat sonar), camouflage (Satanic leaf gecko), or molecular (enzyme-substrate fit).

Sexual Selection

• Traits directly increase reproductive success.
• Sexual dimorphism emerges, with different phenotypes in males and females.

Intersexual Selection

• Members of one sex (typically females) choose mates of the other sex (typically males).
• Male displays (turkey tail feathers, peacock plumage) signal attractiveness.
• This leads to selection for specific traits, such as colorful plumage in males.

Intrasexual Selection

• Competition occurs between males for control of females or breeding territories.
• Males become aggressive, large, and strong (e.g., elephant seals).

Phenotype Distribution

• Most characteristics follow a bell curve of continuous variation in a population.
• Directional selection selects against one extreme, shifting the population in one direction.
• Stabilizing selection selects against both extremes, favoring the average phenotype (e.g., birth weight in babies).
• Disruptive selection favors both extremes, splitting the population if the average phenotype is maladaptive.

Adaptive Melanism

• Darkening of the body within a population occurs in response to environmental darkening.
• It happens over evolutionary time, not within an individual.
• Predation typically drives this selection.
• The rock pocket mouse is an example where populations on dark substrates evolved a mutation for increased melanin production.

Evolutionary Fitness

• Fitness is measured by the number of offspring and subsequent generations that survive to reproduce.
• It applies at every level of the life cycle.

Peppered Moth Example

• The peppered moth demonstrates directional selection and adaptive melanism due to environmental change.
• Two forms exist: peppered (light) and dark.
• Before the Industrial Revolution, the peppered form predominated due to camouflage on light-colored tree trunks covered with lichens.
• Industrial Revolution soot darkened tree trunks and killed lichens, giving a selective advantage to dark-colored moths.
• As pollution declined, the trend reversed, with the peppered form becoming more common again.
• Research by Michael Majerus confirmed this case of adaptive melanism.

Population Genetics

• Population genetics studies gene distribution and changes in populations over time.
• Allele frequency is a key measurement.
• A gene pool consists of all alleles of all genes in a population.
• Evolution is the change in allele frequencies within a gene pool over time.
• The misconception that a dominant allele must be more common than a recessive allele is incorrect.
• Allele frequency depends on the advantage or harm conferred by the phenotype and random historical factors.
• Achondroplasia is an example of a rare, but dominant allele.

Hardy-Weinberg Equations

• The field is built around two equations: p + q = 1 and p² + 2pq + q² = 1.
• p represents the frequency of the dominant allele.
• q represents the frequency of the recessive allele.
• p + q = 1 means that the sum of dominant and recessive allele frequencies equals 100% of alleles for a gene.
• p² + 2pq + q² = 1 represents the distribution of genotypes: homozygous dominant (p²), heterozygous (2pq), and homozygous recessive (q²).
• Setting up Punnett squares of population allele frequencies gets the correct probabilities.

Hardy-Weinberg Principle

• Allele frequencies in a gene pool remain constant unless certain conditions are not met.
• Conditions for Hardy-Weinberg equilibrium: infinitely large population, no harmful or beneficial alleles, random mating, no gene flow, and no net mutation.
• Violation of these conditions can cause evolutionary change.

Factors Causing Evolution

• Small populations lead to genetic drift.
• Natural selection favors beneficial alleles.
• Non-random mating occurs.
• Gene flow moves genes in or out of a population.
• Directional mutation changes allele frequencies.

Genetic Drift

• Random change in allele frequencies occurs in a population's gene pool, especially in small populations.
• A population bottleneck, caused by biotic or abiotic factors, can cause genetic drift which wipes out of most of the population.
• Cheetahs are genetically uniform.

Founder Effect

• A small group founds a new population.
• Allele frequencies among founders may differ from the parent population due to sampling bias.

Gene Flow

• The movement of alleles from one population to another.
• This can involve the movement of individuals or gametes.
• Gene flow changes allele frequencies and diminishes differences between adjacent populations.

Mutation

• Mutation is the ultimate source of genetic variation.
• It changes allele frequencies within a population if it is directional.

Sickle Cell Disease Example

• Sickle cell disease results from a recessive allele in the hemoglobin gene.
• Heterozygotes have a small amount of sickling.
• Heterozygotes are resistant to malaria.
• Homozygous dominant individuals are susceptible to malaria.
• Homozygous recessive individuals experience sickle cell disease.
• This is a case of heterozygote advantage, maintaining the sickle cell allele in malaria-prone regions.
• This model may apply to other genetic diseases like cystic fibrosis and Tay-Sachs.

Evidence of Evolution

• Homologous traits are the most important evidence.
• These are traits that share a common underlying structure and embryological origin, showing descent with modification.
• The forelimbs of humans, dogs, birds, and whales are examples.
• Homologous features result from adaptive radiation.
• A parent species produces several descendants, each with unique adaptations, where they fill distinct ecological niches.
• Galapagos finches exemplify adaptive radiation.

Vestigial Structures

• Vestigial structures are special homologies with no apparent function.
• They're inherited from ancestors.
• Whales have pelvic bones without hind limbs.
• Humans have a coccyx (tailbone).

Homology vs. Analogy

• Analogous features have a similar function but different underlying structure, arising through convergent evolution.
• Sharks, ichthyosaurs, and dolphins have a hydrodynamic form as a convergent solution to swimming.
• Bird and bat wings are analogous for flight, but the bones in the forelimbs of birds and bats are homologous.

Molecular Homologies

• Molecular homologies occur at the molecular level.
• Molecules indicate common ancestry through structure and monomer sequence.
• All vertebrates have hemoglobin with a shared structure.
• Amino acid sequence differences in hemoglobin correlate with evolutionary distance.

Pseudogenes

• Non-functional genes are variants of functional genes in related species.
• Humans have a non-functional GULO gene.
• This is a molecular vestigial feature resulting from descent with modification.
• GULO pseudogenes in different species (guinea pigs, bats) have different mutations, indicating convergent evolution.

Universal Molecular Homologies

• DNA as genetic material, ATP for energy, universal genetic code, ribosomes for protein synthesis, and shared metabolic pathways (glycolysis, Krebs cycle, etc.).

Eukaryotic Homologies

• Nucleus, mitochondria, endomembrane system, genes with introns, linear chromosomes, and sexual reproduction.

Embryological Development

• Early vertebrate embryos resemble each other.
• Embryos differentiate, adopting adult body forms of their lineage.
• Similar embryonic forms indicate common ancestry.
• Embryos show vestigial features (tail in humans, pharyngeal gill slits) indicating descent with modification.

Shared Genes for Animal Development

• Diverse species share conserved genes for development.
• The eyeless gene controls eye development in arthropods and vertebrates.
• Homeotic genes control body plan and segmentation.

Biogeography

• Biogeography studies the geographic distribution of species.
• Distribution patterns fit the idea that populations evolve in one area, then spread to adjacent regions.
• Marsupials predominantly live in Australia due to its isolation and limited placental mammal dispersal.

Parallel Evolution

• Placental mammals never spread to Australia.
• Marsupials fill similar ecological niches in Australia.
• Marsupial and placental moles, sugar gliders and flying squirrels, and the Tasmanian wolf and placental wolves all demonstrate convergent similarities evolved from filling the same archetypes in their environments.

Fossils

• Fossils are petrified remains of living things.
• They demonstrate change over time.
• Transitional forms show descent with modification.
• Fossil records show ancestors of modern species.

Relative Dating

• Relative dating uses superposition.
• Younger material lies over the older in sedimentary rocks.
• Faulting, uplift, and inversions complicate analysis.

Absolute Dating

• Absolute dating uses the decay of radioactive isotopes.
• Half-life is the time for half of a sample to decay.
• Carbon-14 decays to nitrogen-14 with a half-life of 5,730 years.
• Isotopes in volcanic strata are used to date older fossils.

Evolution of Resistance

• Evolution of resistance to DDT in mosquitoes is evidence of continuing evolution.
• DDT kills most mosquitoes, but resistant ones survive.
• These resistant mosquitoes pass on genes for resistance.
• Over time, mosquitoes become more resistant to DDT.
• Parallel instances are antibiotic resistance in bacteria, herbicide resistance in weeds, and chemotherapy resistance in cancer cells.### Speciation and Extinction
• The biological species concept defines a species as a group of organisms that can naturally interbreed.
• Offspring must be viable (healthy) and fertile (able to reproduce).
• Species must be reproductively isolated from other such groups.
• Dogs are one species despite different breeds as they can interbreed.
• Certain duck species don't interbreed enough to mix their gene pools.
• The biological species concept isn't perfect.
• Closely related species can sometimes hybridize.
• The concept doesn't apply to extinct or asexual species.
• The concept doesn't apply to prokaryotic species.

Reproductive Isolating Mechanisms

• Reproductive isolating mechanisms are processes, behaviors, or traits that keep gene pools of closely related species separate.
• Prezygotic isolating mechanisms prevent breeding and zygote formation.
• Postzygotic barriers allow mating and zygote formation, but the zygote doesn't lead to successful, viable offspring.

Prezygotic Isolating Mechanisms

• Behavioral isolation is where different mating rituals or courtship behaviors would keep a female and a male from accepting one another as members of the same species
• Temporal isolation is one species mates in the winter another mates in the summer they're not going to breath
• Mechanical isolation is where structural barriers prevent sperm or pollen from reaching an egg.
• Habitat isolation is One species lives in the forest another lives in a meadow, one species lives in the Uplands another lives in the lowlands they won't meet each other in order to breed
• Gametic isolation is where the egg won't allow fertilization because because there's some molecular mismatch that would keep the sperm from being able to bind with the egg and induce the kind of changes that lead to fertilization

Postzygotic Isolating Mechanisms

• Hybrid inviability occurs when hybrid organisms don't develop.
• Hybrid sterility occurs when hybrid offspring are healthy but can't reproduce (e.g., mules).
• Hybrid breakdown occurs when hybrids are healthy and can reproduce, but the next generation (F2) are inviable or infertile.

Allopatric vs. Sympatric Speciation

• Allopatric speciation involves a geographic barrier.
• Sympatric speciation occurs without a geographic barrier.
• Allopatric speciation: geographic isolation leads to genetic differentiation, then reproductive isolation.
• Stage 1: species spread over a range with gene flow.
• Stage 2: geographic barrier arises, splitting the species and stopping gene flow.
• Stages 2 & 3: environmental differences cause different selective pressures and genetic differentiation.
• Barrier disappears: formerly subspecies are too different to interbreed.
• Sympatric speciation in plants can occur through polyploidy(changes in chromosome numbers).
• Sympatric speciation in animals can occur through sexual selection.
• Adaptation to specific microhabitats can also lead to sympatric speciation (e.g., lice on birds).

Adaptive Radiation

• Adaptive radiation occurs when one parent species produces several descendant species.
• Each descendant has unique adaptations and fills a different ecological niche.
• The 14 species of Galapagos finches are an example of adaptive radiation from a single South American species.
• Phylogeny reflects adaptive radiation.
• Homologous and vestigial traits result from adaptive radiation.

Importance of Phenotypic Variation

• Phenotypic variation is essential for evolution, as it's the raw material upon which natural selection acts.
• Natural selection selects for organisms with advantageous phenotypes.
• The genotype is invisible to natural selection; it acts upon the phenotype.
• Individuals with advantageous phenotypes survive and reproduce at higher rates.
• Without phenotypic variation, there can be no natural selection or adaptation.
• Loss of variation is dangerous to a species and can lead to extinction.
• Mammals in snowy environments have more saturated phospholipid tails in the body core and more unsaturated tails in the extremities.
• Fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin.
• Chlorophyll A absorbs more red light, best in direct light
• Chlorophyll B absorbs more blue light, best in indirect light or shady environments

Extinction

• Extinction is a normal part of the process of life.
• Greater than 99% of all species that have ever lived have become extinct.
• Extinction Vortex: population decline leads to genetic drift, loss of diversity, reduced fitness, and smaller population repeating the cycle.
• Mass Extinction: widespread, rapid decrease in Earth's biodiversity.
• Often caused by geological or astronomical events.
• There have been at least five major extinction events in the last 600 million years.
• Mass extinction leaves vacant ecological niches.
• Adaptive radiation follows mass extinction.
• Diversification of placental mammals followed the Cretaceous Extinction.
• Humans are causing the sixth extinction.
• Human activities causing extinction include: habitat destruction/fragmentation, overhunting/harvesting, and introducing invasive species.

Phylogeny

• Phylogeny means evolutionary history
• A phylogenetic tree is a branching diagram that shows evolutionary relationships.
• Trees are built using morphological, molecular, or genetic evidence
• The claim is that hippos and whales are more closely related to one another than whales are to Deer because based on the evidence, hippos and whales have a more recent common ancestor than either does with deer we'll see the details in the subsequent slides

Clade

• A clade is a group of organisms that consists of a common ancestor and all of that ancestor's descendants.
• All members of a species have a common ancestor

Shared Derived Character

• A shared derived character is a trait that identifies/distinguishes a clade.
• It evolved in the common ancestor of that clade and sets it apart from other clades.
• For example lungs and four limbs separate organisms classified as frogs ards alligators Robbins rats and gorillas

Nodes and Sister Group

• A node is where two branches in a phylogenetic tree diverge
• Nodes represent the common ancestor of the two diverging lineages
• Sister groups are descendants that split apart from the same node

Outgroup

• An outgroup is a more distantly related group of organisms that's used to determine the evolutionary relationships among the other organisms in the tree which is the ingroup.
• It's a point of comparison for the ingroup and it's a species or it's some other taxonomic category that's not part of the clade to which all the other organisms in the phylogenetic tree belong

Mistakes to avoid

• Do not think that that vertical closeness on a horizontal tree indicates evolutionary closeness.
• The only thing that matters on a philogenetic tree in terms of evolutionary relatedness is the recency of common ancestry

Ancestral Feature

• An ancestral feature is a trait that members of a clay share but which is also shared by larger more inclusive clades; it doesn't define the clay

Building Phylogenetic Trees

• Before the 1960s, morphological similarities were used to construct phylogenetic trees.
• Since the 1960s, nucleotide sequences in DNA and RNA, and amino acid sequences in proteins are used
• DNA analysis would indicate that the common Cactus Finch is more closely related to the large ground finch than to any of the other Galapagos species that's a hypothesis and you could confirm that through DNA sequencing

Molecular Clocks

• For any specific protein or nucleic acid, the rate of change caused by accumulated mutations is constant over time.
• Helps calibrate the amount of change in a gene or protein to when species split apart.

Origin of Life

• Main question: How did life emerge naturally?
• Pertains to the Cell Theory and the first cell emergence.
• How did complex substances that life is based on emerge in the absence of enzymes.
• Earth is 4.5 billion years old.
• Life emerged about 3.8 billion years ago

Key Steps for Life's Emergence

• Earth needed to become a habitable and more stable planet.
• Monomers had to start to emerge abiotically.
• There needs to be some kind of abiotic process by which that could happen, where we have the abiotic synthesis of polymers from monomers and the formation of vesicles those are goings to become the little capsules into which cells will emerge in step four.
• Combination of monomers and polymers into vesicles to create protocells (not quite living cells)
• Emergence of self-replicating cells (last universal common ancestor)
• Miller-Urey experiment (1950s) showed that amino acids could be synthesized abiotically in a simulated early Earth environment.

The Miller-Urey Experiment Setup

• A sterile apparatus with chambers, tubing, sealed off, and sterile
• An area representing the early oceans that was heated with a bunson burner
• Gases that were supposed to be present in the early atmosphere like methane, ammonia, hydrogen, and water vapor were loaded into the atmosphere
• Electrodes which simulated lightning
• Gases circulated through a condenser and trapped whatever was caught without contaminating the apparatus sample-able areas.
• Miller who was the actual experiment sampled the liquid and they found the presence of amino acids

RNA World

• RNA, not DNA, was the first hereditary molecule.
• RNA stores genetic information and can also act as an enzyme.
• Self-replicating systems of RNA molecules may have emerged as the first genetic molecule system before there were cells.
• Led up to the last Universal common ancestor of Life

Steps Toward Life

• Inorganic precursor molecules (sugars, phosphate, nitrogenous bases) combined via abiotic processes to form RNA monomers.
• Other abiotic non-enzymatic processes would lead to the next step and in that next step we have RNA polymers that start to emerge
• RNAs fold into complex shapes with enzymatic properties.
• Complex shapes cause enzymatic properties that lead systems of rnas
• RNA systems become encapsulated within a lipid bilayer, forming a protocell.
• Further evolution would lead to the emergence of the last Universal common ancestor