Unit 7: Natural Selection, Evolution of Populations, and Phylogeny Notes on Speciation and Phylogeny

Historical Theories of Evolution

• Jean Baptiste Lamarck (1809): Proposed a theory of evolution based on the inheritance of acquired characteristics. His famous example involved the giraffe: an original short-necked ancestor would continually stretch its neck to reach leaves higher up in a tree, and through this constant stretching, its neck would become progressively longer over its lifetime, a trait passed to offspring.

• Charles Darwin and the Voyage of the HMS Beagle (1831): Darwin traveled around the world, making significant observations in South America, Great Britain, Africa, and Australia. His most notable stop was the Galápagos Islands.

• Galápagos Finches: Darwin observed a variety of finches with specialized beaks adapted to specific food sources:

  • Tree Finches (Grasping bills): Includes small insectivorous, large insectivorous, and woodpecker finches (insect eaters), as well as vegetarian tree finches (fruit eaters).

  • Ground Finches (Crushing bills): Includes cactus ground finches (cactus eaters) and small, medium, and large ground finches (seed eaters).

  • Warbler Finches (Probing bills): Specialized for eating insects.

• On the Origin of Species (1859): Darwin published his findings under the full title "On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life."

Principles of Natural Selection

• The Four Steps of Natural Selection:

  1. Variation: There is genetic variation within a population that can be inherited (e.g., color differences in beetles).

  2. Competition (Overproduction): Populations produce more offspring than the environment can support, leading to competition for survival.

  3. Adaptations (Selection): Individuals with beneficial adaptations (favorable mutations) are more likely to survive and pass on their genes.

  4. Evolution: Over many generations, there is a change in allele frequency within the population.

• Key Elements of Evolution:

  1. Populations evolve, NOT individuals.

  2. Natural selection can only act on existing genetic variation.

  3. Natural selection cannot produce "perfect" organisms; it is limited by historical constraints.

• Evolutionary Fitness: Measured by an organism's ability to survive AND produce healthy, fertile offspring.

• Selective Pressures: Any force that favors one variation over another, such as environmental stress, which gives certain organisms an "edge."

Artificial Selection and Real-World Examples

• Artificial Selection (Selective Breeding): Humans modify species by selecting for specific traits. Examples include the diversification of the wild mustard plant into:

  • Kohlrabi: Selection for the stem.

  • Kale: Selection for leaves.

  • Broccoli: Selection for flowers and stems.

  • Brussels sprouts: Selection for lateral buds.

  • Cabbage: Selection for the terminal bud.

• Pesticide Resistance: An application of a pesticide may kill most insects, but survivors possessing a chromosome with an allele conferring resistance will reproduce. Subsequent applications become less effective as the frequency of resistant insects grows.

• Rapid Evolution of the Peppered Moth: A classic example showing how environmental changes (industrial soot) shifted selection from light-colored to dark-colored moths.

Evidence for Evolution

• Fossils and Rock Layers:

  • Law of Superposition: Younger rocks are found on top of older rocks.

  • Fossil Records: Show transitional forms, such as the evolution of whales from terrestrial ancestors: Pakicetus (terrestrial) → Rodhocetus (predominantly aquatic) → Dorudon (fully aquatic) → Balaena (recent whale ancestor).

• Homologous vs. Analogous Structures:

  • Homologous Structures: Different functions but similar structures due to a common ancestor (e.g., human arm, cat leg, whale flipper, bat wing—all share humerus, radius, ulna, carpals, metacarpals, and phalanges).

  • Analogous Structures: Same function but different structures, evolved separately (e.g., bird wing vs. insect wing).

• Vestigial Structures: Remnants of features that served important functions in ancestors but are now marginal or useless (e.g., human appendix, cecum, and coccyx/tail bone).

• Molecular Biology: Comparisons of DNA and protein sequences. The number of amino acid differences in Cytochrome c compared to humans reveals evolutionary distance:

  • Chimpanzee: $0$

  • Rhesus monkey: $1$

  • Rabbit: $9$

  • Cow: $10$

  • Pigeon: $12$

  • Bullfrog: $20$

  • Fruit fly: $24$

  • Wheat germ: $37$

  • Yeast: $42$

The Hardy-Weinberg Equilibrium

• Purpose: Predicts allele and genotype frequencies for a non-evolving population. It serves as a null hypothesis to determine if evolution is occurring.

• The Hardy-Weinberg Equations:

  • $p + q = 1$

  • $p^2 + 2pq + q^2 = 1$

  • $p$ = frequency of allele 1 (dominant)

  • $q$ = frequency of allele 2 (recessive)

  • $p^2$ = frequency of homozygous dominant genotype

  • $2pq$ = frequency of heterozygous genotype

  • $q^2$ = frequency of homozygous recessive genotype

• The Five Assumptions of Hardy-Weinberg:

  1. The population is very large.

  2. There is random mating.

  3. There are no new mutations.

  4. There is no gene flow (migration).

  5. There is no natural selection.

• Practice Problem (Tongue Rolling): If $64\%$ are nonrollers ($rr$), then $q^2 = 0.64$. Therefore, $q = \sqrt{0.64} = 0.8$. Using $p + q = 1$, we find $p = 1 - 0.8 = 0.2$. Genetic frequencies are $p = 0.2$ and $q = 0.8$.

Mechanisms of Microevolution

• Microevolution: A change in allele frequency within a population from generation to generation.

• Five Mechanisms:

  1. Natural Selection: Differential survival based on phenotype.

  2. Sexual Selection: Selection based on mating success, often leading to Sexual Dimorphism (distinct differences between sexes).

  3. Genetic Drift: Random changes in allele frequencies, most impactful in small populations.

     • Bottleneck Effect: Occurs when a population size is drastically reduced (e.g., American bison population dropped from $60,000,000$ before 1492 to only $750$ in 1890).

  4. Gene Flow: Migration of individuals between populations.

  5. Relatively Constant Allele Shuffling: Sexual reproduction (segregation and fertilization) alone does not change allele frequencies; other factors must be at play.

• Patterns of Natural Selection:

  • Directional Selection: Shifts variation in one specific direction.

  • Stabilizing Selection: Favors intermediate (middle) forms.

  • Disruptive Selection: Favors forms at both extremes of the range.

• Balancing Selection: Maintains two or more phenotypic forms in a population.

  • Heterozygote Advantage: Example: Sickle Cell anemia. Carrying one sickle cell allele provides protection against severe Plasmodium falciparum malaria through reduced "rosetting."

  • Frequency-Dependent Selection: The fitness of a phenotype depends on how common it is (e.g., "left-mouthed" vs. "right-mouthed" fish).

Speciation and Reproductive Barriers

• Species Concepts:

  • Biological: Defined by reproductive isolation.

  • Morphological: Based on physical traits (size, shape).

  • Ecological: Based on the role in the biological community.

  • Phylogenetic: Smallest group sharing a common ancestor.

• Types of Speciation:

  • Allopatric Speciation: Geographic barriers (like a canyon or mountain range) physically isolate populations.

  • Sympatric Speciation: Speciation occurs within the same geographic area (e.g., driven by pollinator choice in monkey flowers, M. lewisii and M. cardinalis).

• Reproductive Barriers:

  • Prezygotic (Before the zygote): Geographic, Habitat, Temporal (time-based), Behavioral, Mechanical, and Gametic isolation.

  • Postzygotic (After the zygote): Low hybrid viability and low hybrid fertility (sterile offspring).

• Adaptive Radiation: A period of rapid diversification from an ancestral species into many new species (e.g., Galápagos finches).

The Origin and History of Life

• Abiogenesis (The Four Stages):

  1. Abiotic synthesis of organic monomers.

  2. Abiotic synthesis of polymers.

  3. Formation of pre-cells (membrane-enclosed compartments).

  4. Self-replicating molecules (RNA world; Ribozymes acting as simple "genes").

• Miller-Urey Experiment (1953): Simulated early Earth conditions (Water vapor, $CH_4$, $NH_3$, $H_2$, and sparks for lightning) to produce amino acids. Re-analysis in 2008 found significantly more amino acids than originally identified.

• Geologic Timeline:

  • $4.6$ billion years ago (bya): Origin of Earth.

  • $3.8$ bya: Oldest evidence of prokaryotic cells.

  • $2.7$ bya: Atmospheric oxygen begins to accumulate due to single-celled autotrophs.

  • $2.0$ bya: First eukaryotes (endosymbiosis of mitochondria).

  • $900$ million years ago (mya): First multicellular life.

  • $540$ mya: Cambrian Explosion (rapid diversification).

  • $488$ mya: Land plants appear.

  • $250$ mya: Earth's 3rd and largest mass extinction (volcanic activity, $96\%$ species loss).

  • $65$ mya: Earth's 5th mass extinction (asteroid impact, extinction of dinosaurs).

  • $200,000$ years ago (ya): First Homo sapiens.

Phylogeny and Molecular Systematics

• Phylogenetic Trees: Family trees showing common ancestors and descendants over time. The "root" is the ancestor; "tips" are descendants.

• Clades (Monophyletic Groups): A grouping that includes a common ancestor and ALL of its descendants.

  • Paraphyletic: Includes common ancestor and some, but not all, descendants.

  • Polyphyletic: Does not include the common ancestor of the group.

• Parsimony: The simplest explanation based on available data is typically preferred in tree building.

• Molecular Evidence Case Study: Vitamin C & Scurvy:

  • Humans, other primates, guinea pigs, and fruit bats cannot synthesize Vitamin C because they lack the functional GULO enzyme (L-gulonolactone oxidase).

  • In animals like mice and cows, the GULO gene is functional due to natural selection preventing mutations in a necessary protein.

  • In humans, the GULO gene is present but highly mutated (pseudogene) because Vitamin C was readily available in the diet, making the gene unnecessary for survival. If the diet lacks Vitamin C, scurvy occurs. This loss of ability occurred separately in three different mammalian lineages (convergent evolution).

Human Evolution (Hominins)

• Key Hominin Species:

  • Sahelanthropus tchadensis ($7-6$ mya): Early adaptations for bipedalism.

  • Ardipithecus ($5.8-4.4$ mya).

  • Australopithecus afarensis ("Lucy").

  • Homo habilis ($2.4-1.6$ mya): Larger brain ($600\,cc$), used stone tools.

  • Homo erectus ($1.8\,mya - 143,000\,ya$): Brain size $650-1200\,cc$, long legs for walking.

  • Homo neanderthalensis: Large brains ($1400\,cc$), sophisticated tools, distinct cranial features (browridge, receding forehead).

  • Homo sapiens: Rounded cranial vault, small brow-ridges, capacity for symbolic thought and language.

Questions & Discussion

• Question: How does blood type relate to evolution?

• Response: Studies show the ABO blood group evolved at least $20$ million years ago. Blood group O has been found to provide protection against severe malaria by reducing rosetting. Recent studies have also investigated links between blood type and COVID-19 severity, though some findings have been debunked. Cultural stereotypes about blood types (e.g., in Japan) could influence sexual selection, though this is considered pseudoscience.