Bio Midterm PDF

Chapter 22: Darwin & Descent with Modification Myth Busting: Evolution ​ Evolution is a theory about the origin of life → False ○​ Evolution explains how life changes after its origin, not how it began. ○​ Abiogenesis: Processes that led to the origin of life. ○​ Sci...

Chapter 22: Darwin & Descent with Modification Myth Busting: Evolution ​ Evolution is a theory about the origin of life → False ○​ Evolution explains how life changes after its origin, not how it began. ○​ Abiogenesis: Processes that led to the origin of life. ○​ Scientific hypothesis suggests a gradual transition from non-living to living: ○​ Key steps: ​ Prebiotic synthesis of small organic molecules (sugars, lipids, nucleobases, peptides). ​ Molecular self-replication (e.g., RNA). ​ Self-assembly (e.g., protocells). ​ Evolution is a climb up a ladder of progress → False ○​ Evolution is about reproductive fitness, not progress. ○​ Natural selection eliminates individuals with lower reproductive success in a given environment. ○​ Many taxa (e.g., mosses, fungi, corals, crayfish) have changed little over long periods. ○​ Example: Stromatolites (oldest fossils, ~3.5 billion years old). ​ Evolution is entirely random → Partially false ○​ Random mutations are the ultimate source of genetic variation. ○​ However, evolutionary change is limited by environmental conditions. ○​ Only heritable variations that improve population fitness persist. ​ Natural selection involves organisms trying to adapt → False ○​ This is Lamarck’s view (early 19th century, pre-Darwin) ○​ Lamarck’s evolutionary view: ​ "Inheritance of acquired characteristics" ​ "Use and disuse": ​ Frequently used body parts→ stronger/more developed. ​ Unused body parts → deteriorate over time. ○​ Rejected because: ​ Traits are passed through genes, not acquired characteristics. ​ "Use and disuse" implies rapid adaptation, but vestigial structures show long-term evolutionary processes. ○​ Example: Blind Mexican tetra (Astyanax mexicanus): ​ Lives in total darkness. ​ Lost functional eyes (only empty sockets remain). ​ Instead, it developed sensory organs along its body with enhanced smell and touch. ​ Natural selection gives organisms what they need → False ○​ Natural selection has no intentions or senses. ○​ If genetic variation allows survival under stress → those individuals reproduce more → population evolves. ○​ Without genetic variation, natural selection does nothing.  ​ Evolution is just a theory → True ○​ In science, a theory is a well-substantiated explanation backed by multiple lines of evidence. ○​ Evolutionary theory: ​ Life has existed for billions of years and changed over time. ​ Change occurs through descent with modification by natural selection. Descent with Modification ​ Historical Roots Leading to Darwin’s Proposal ○​ Individuals vary within populations ○​ Artificial selection practiced for thousands of years ○​ Time: Enormous amounts (Hutton, Lyell) ○​ Species change (Lamarck) ○​ Species have gone extinct (Cuvier) ○​ Observations matter (Vesalius) ○​ Species have potential for unlimited growth, but do not (Malthus) ​ Descent with Modification by Natural Selection ○​ In limited environments, individuals with better traits leave more offspring ○​ If traits are hereditary, they become dominant → evolution by natural selection ○​ Earth/environment changes over time → species must adapt or go extinct ○​ Adaptation leading to reproductive isolation results in new species ​ Darwin (1809–1882) ○​ Did not know the source of variation (now known as germ-cell mutations) Lines of Evidence for Evolution ​ Direct Observations ○​ Invasive species and drug-resistant bacteria ○​ Pesticide Resistance ​ 1st Gen: Toxic heavy metals (lead, arsenic, mercury) ​ 2nd Gen: Organochlorines (DDT) → resistance increased ​ 3rd Gen: Pyrethroids, insect growth regulators, neonicotinoids → resistance, environmental effects (e.g., bee decline) ​ 4th Gen: GMOs (Bt crops), RNA interference → concerns over biotech use ​ Homology & Vestigial Structures ○​ Similar structures in different species show common ancestry ​ Fossil Record ○​ Transitional species: Pakicetus (early whale ancestor, 50 Ma), Tiktaalik (transition from water to land, 375 Ma) ​ Biogeography ○​ Geographic distribution of species reflects evolutionary history Chapter 23: Evolution of Populations (Microevolution) Source of New Variations  ​ Mutation: ○​ 3.5 mL @ 300 M/mL = approx. 1 B sperm. ○​ 1 gamete mutated in 100,000 to 1 M. ○​ 1,000 to 10,000 sperm mutated at that locus. ○​ 20,000 protein-coding genes → only 1.5% of the human genome. ○​ Odds: 1 in 50 to 1 in 5 sperm carries mutation. ○​ Mutation effects: neutral, deleterious, lethal, advantageous. ​ Chromosomal Changes (Meiosis) ○​ Translocation, deletion, duplication, inversion, isochromosome, fusion. ​ Sexual Reproduction: ○​ Recombination/Crossing Over (Prophase I): ​ Homologous chromosomes (one from each parent) align → form bivalent or tetrad. ​ Non-sister chromatids physically cross over at chiasmata and reattach. ​ Creates new allele combinations → genetic uniqueness. ○​ Independent Assortment (Metaphase I & Anaphase I): ​ Homologous tetrads line up randomly on the metaphase plate. ​ Each tetrad can align in two ways → maternal or paternal chromosome toward a given pole. ​ Separation → homologs pulled to opposite poles. ​ 2ⁿ combinations (e.g., humans: n = 23 → 2²³ = 200 billion trillion possible combinations). ○​ Fertilization: ​ Random fusion of gametes further increases variation. Genetic Variation in Populations ​ Heterozygosity (H) = 2pq ○​ measure of population variation at a single locus. ​ Genotypic Frequency: ○​ (p + q + r)² = p² + q² + r² + 2pq + 2pr + 2qr. ​ Average Heterozygosity (Havg): ○​ Heterozygosity at a single locus does not represent overall variation. ○​ Need heterozygosity averaged over many loci. Hardy-Weinberg ​ Equilibrium and Evolution ○​ If allele frequencies (p & q) remain constant across generations → Hardy-Weinberg Equilibrium → no evolution occurs. ○​ If allele frequencies (p & q) change from one generation to the next, at least one assumption is compromised, and Hardy-Weinberg Equilibrium no longer applies. ○​ Changing allele frequencies between generations indicates evolution at work, specifically microevolution. ​ Factors That Disrupt Hardy-Weinberg Equilibrium ○​ Genetic Variation Through Mutations ​ Assumption: No mutations occur ​ Why it's wrong: Mutations do occur  ​ Cause: Mutations are a source of genetic variation. ○​ Gene Flow and Population Mixing ​ Assumption: No immigration ​ Why it's wrong: Immigration does occur ​ Cause: Gene flow brings alleles from different populations, altering allele frequencies. ○​ Population Size and Genetic Drift ​ Assumption: Large population size ​ Why it's wrong: Small population size leads to genetic drift, causing random fluctuations in allele frequencies. ​ Cause: Genetic drift causes allele frequencies to change by chance, reducing genetic diversity. ​ Leads to loss of genetic diversity and fixation of alleles. ​ Bottleneck Effect: A sudden reduction in population size reduces genetic diversity. ​ Founder Effect: A small group establishes a new population with different allele frequencies than the original. ○​ Differential Survival and Natural Selection ​ Assumption: All genotypes have equal fitness ​ Why it's wrong: Genotypes differ in fitness ​ Cause: Natural selection acts on traits that improve an organism’s reproductive success. ​ Changes in environmental pressures influence survival. ​ Phenotypes that are more fit leave more offspring. ​ Leads to gradual population change over generations. ​ Adaptive Evolution: Traits enhancing survival or reproduction increase in frequency. ​ Evolution by natural selection is a mix of chance and sorting: ​ Chance: Creates new genetic variations (mutations). ​ Sorting: Natural selection favors certain alleles. ​ Natural selection is not random because it consistently increases the frequency of beneficial alleles. ​ Directional Selection: Favors one extreme phenotype. ​ Stabilizing Selection: Favors intermediate phenotypes. ​ Disruptive Selection: Favors both extreme phenotypes. ○​ Mating Patterns and Nonrandom Mating/Inbreeding ​ Assumption: Mating is random ​ Why it's wrong: Non-random mating or inbreeding alters genotype frequencies. ​ Cause: Nonrandom mating/inbreeding affects the distribution of alleles in a population. ​ In small populations, random selection leads to genetic drift. ​ Heterozygote Advantage: Maintains genetic diversity by favoring heterozygous individuals.  ​ Frequency-Dependent Selection: Fitness of a phenotype depends on its frequency in the population. ​ Habitat Selection: Certain traits are favored based on environmental conditions. Chapter 24: Speciation Biological Species Concept ​ Morphological species ○​ Are distinct in form and structure from other groups ○​ Practical for fossil record; academic field guides ○​ But morphological similarities can be misleading (convergent evolution) ​ Ecological species ○​ Share distinct resources; share the same niche ○​ Relevant towards ecosystem modeling ​ Biological species ○​ Defined by the ability to interbreed in nature and produce fertile offspring ​ Key factor: Reproductive isolation, preventing gene flow between populations ○​ Prezygotic Barriers (Prevent Mating or Fertilization) ​ Habitat Isolation: Species live in different environments ​ Temporal Isolation: Species breed at different times ​ Behavioral Isolation: Species have different mating behaviors ​ Mechanical Isolation: ​ Physical differences prevent mating ​ Gametic Isolation: Sperm and egg fail to fuse due to incompatible proteins ○​ Postzygotic Barriers (Prevent Viable or Fertile Offspring) ​ Reduced Hybrid Viability: Embryo fails to develop properly ​ Reduced Hybrid Fertility: Hybrid offspring are sterile ​ Hybrid Breakdown: First-generation hybrids are viable, but their offspring are weak or sterile ○​ Exceptions and challenges ​ Androdioecious Species: Some hermaphroditic species reproduce through self-fertilization (e.g., mangrove killifish) ​ Gynogenetic Species: Females require sperm from another species to trigger egg development but do not incorporate sperm DNA (e.g., Amazon molly) ​ Hybrid Species: Some species interbreed and produce fertile offspring (e.g., ornate butterflyfish hybrid) ​ Ring Species: Connected populations where neighboring groups interbreed, but distant groups do not (e.g., Ensatina salamanders) ○​ Subspecies and Breeds ​ Populations within a species that have genetic and morphological differences  ​ Occupy distinct geographic regions but lack full reproductive isolation ​ Represent early stages of speciation Speciation Without Geographic Separation ​ Allopatric Speciation ○​ Two populations become geographically separated, preventing gene flow ○​ Over time, genetic differences accumulate due to: ​ Mutations ​ Natural selection ​ Genetic drift ○​ Leads to reproductive isolation and formation of new species ​ Parapatric Speciation ○​ Population spans a discontinuous or strongly varying environment ○​ Natural selection favors different alleles on either side of the gradient ○​ Genetic divergence occurs through: ​ Mutations ​ Natural selection ​ Genetic drift ○​ Eventually, reproductive isolation develops ​ Sympatric Speciation ○​ New species arise within the same geographic range ○​ No physical separation, but genetic divergence occurs due to: ​ Mutations ​ Natural selection ​ Genetic drift ○​ Reproductive isolation forms despite shared habitat Hybrid zones ​ Secondary contact ○​ Leads to the formation of hybrid zones, where hybrid offspring can be produced. ​ Hybrid Fitness Decline ○​ Competition between different genotypes compromises cell cooperation, leading to decreased overall fitness. ○​ Highly differentiated species rely on fully functioning body parts, and loss of function in organs or limbs can reduce fitness. ​ Types of Hybrid-related Phenomena ○​ Conjoined Twins: Twins whose bodies become attached during development. ○​ Chimera: Results when two embryos merge at an early stage, leading to a single body with two distinct sets of cells and DNA. ○​ Hybrids: Offspring that have sister chromatids from different species, often displaying features of both species. ​ Hybrid Fitness and Variability ○​ Hybrids may not always lower fitness. ○​ Coral chimera: a colony with distinct genetic lineages, enhances growth and size. ○​ Occurs in the first four months, before allorecognition systems mature. ○​ Increased genetic variability helps adapt to environmental stresses.  ​ Speciation rates ○​ Speciation can be slow (millions of years) or rapid (one generation); involves multiple genes or a single gene. ○​ Macroevolution: large-scale evolutionary changes over long periods, above the species level. ○​ Includes cyclical patterns: ​ Novel adaptations lead to a new common ancestor. ​ Adaptive radiation: rapid diversification from a common ancestor. ​ Extinction of species groups, observed in the geological record. Chapter 25: History of the Earth Eons: larger unit of time than era ​ Hadean (4.6-4.0 billion years ago) ○​ Formation of Earth ○​ Formation of the Moon (collision debris) ○​ Earth’s layer differentiation ​ Heavy elements (iron) → core ​ Lighter silicates → mantle, crust ○​ Early atmosphere ​ Initially: hydrogen, helium which was quickly lost ​ Volcanic outgassing → water vapor, CO₂, methane, nitrogen (reducing) ○​ Liquid water present despite ~230°C surface temperature ○​ Possible RNA synthesis, replication, folding ​ Archean (4.0-2.5 billion years ago) ○​ Geological activity ​ Oldest known rock formations ​ High heat flow (3X to 2X today) → slowing plate tectonics, crustal recycling ​ Intense volcanic activity → maintains reducing atmosphere ​ Magma flows → small proto-continents form ​ Weak, unstable magnetic field → limited UV protection ​ Mostly a water-covered Earth ○​ Abiogenesis ​ Process leading to life remains unknown ​ Transition from nonliving to living was gradual, not a single event (scientific hypothesis) ​ Key stages: ​ Formation of a habitable planet ​ Reducing atmosphere → synthesis of organic molecules (sugars, lipids, nucleobases, peptides) ​ Molecular self-replication (e.g., RNA) ​ Self-assembly into protocells ○​ First evidence of life ​ 3.7 billion-year-old biogenic graphite (Western Greenland)  ○​ First identifiable fossils ​ 3.48 billion-year-old stromatolites (prokaryotic fossils in Australia) ○​ Great Oxygenation Event begins (2.7 billion years ago) ​ Photosynthetic organisms released O₂ into water ​ O₂ reacted with dissolved iron → formation of banded iron formations (BIFs) ​ Once iron was fully precipitated, O₂ began accumulating in oceans → eventually entered the atmosphere ​ Proterozoic ○​ Atmospheric Changes ​ Gassing out of O₂ → methane decline → significant climate and atmospheric shifts ​ Formation of the ozone layer → protection from harmful UV radiation ○​ First major glaciations ​ Huronian glaciation (~2.4–2.1 billion years ago) ​ Possible "Snowball Earth" event → may have influenced the evolution of life ○​ Rise of eukaryotic cells ​ Endosymbiosis and Cellular Evolution ​ Endosymbiosis → led to compartmentalized cellular structures ​ Prokaryotic features: ○​ Nucleoid ○​ Ribosomes ​ Key Structural Changes ​ Evagination of cellular membrane ​ Formation of nucleus & endoplasmic reticulum ​ Role of Gram-Negative Bacteria ​ Engulfed as undigested prey or internal parasite ​ Host & endosymbiont relationship: ○​ Became increasingly interdependent ○​ Eventually formed a single organism → first eukaryotic cell ​ Fossil Evidence ​ 1.8 billion years ago → earliest known eukaryotic fossil ​ 1.3 billion years ago → emergence of multicellular eukaryotes ​ 890 million years ago → sponge-like Porifera biomarkers ​ 575 million years ago → Ediacaran biota (soft-bodied, unambiguous fossils) ​ 555 million years ago → Trace fossils (burrows and tracks indicating mobility) ○​ End of the Proterozoic ​ Ocean chemistry changes → Increased nutrient availability and deep-water oxygenation ​ Oxygen levels → Increased to near modern levels, likely due to secondary endosymbiosis  ​ Biological impact → Higher O₂ concentrations supported more complex, energy-demanding life forms ​ Environmental changes → Baykonur Glaciation event, breakup of supercontinent Pannotia ​ Extinction event → Ediacaran species declined due to environmental shifts and competition with emerging life forms ​ Phanerozoic ○​ Current geological exon ○​ Split into 3 eras: ​ Paleozoic (541-252 Ma) ​ Mesozoic (252-66Ma) ​ Cenozoic (66Ma- today) Eras: ​ Paleozoic (541-252 Ma) ○​ Periods: ​ Cambrian (541-485 Ma) ​ Rapid appearance of complex organisms ​ Bilateral symmetry, segmented bodies, limbs → improved mobility ​ Development of hard body parts (shells, exoskeletons, spines) → protection and support ​ Most major animal phyla appeared ​ Established trophic structures and ecological dynamics ​ Terms to know: ​ Colonization of Land (~500 Ma) ​ Algae and bacterial mats were the first life forms on land. ​ Key Evolutionary Challenges ​ Desiccation → Avoiding water loss ​ UV Radiation → Protection from sunlight ​ Gas Exchange → Efficient oxygen and carbon dioxide exchange ​ Structural Support → Maintaining shape without water buoyancy ​ Nutrient Acquisition → Extracting nutrients from soil  ​ Reproduction Without Water → Adapting to dry conditions ​ Mobility and Dispersal → Spreading across land ​ Ordovician (485-443 Ma) ​ Jawless fish and coral reefs dominated ​ First primitive land plants emerged ​ Silurian (443-419 Ma) ​ First jawed fish appeared First vascular plants evolved ​ First terrestrial arthropods (insects, scorpions) colonized land ​ Devonian (419-359 Ma) ​ "Age of Fishes" → diverse fish species evolved ​ First forests and seed-bearing plants appeared ​ First tetrapods (amphibians) and flying insects emerged ​ Carboniferous (359-299 Ma) ​ Lush vegetation, extensive coal swamps ​ Amphibians thrived ​ First reptiles evolved ​ Permian (299-252 Ma) ​ Formation of supercontinent Pangea ​ Ended with the Permian-Triassic Extinction (~90% marine, ~70% terrestrial species extinct ○​ Paleozoic Collapsed ​ Pangea formation → Loss of shallow water habitats ​ Siberian Traps volcanic activity ​ Massive CO₂ and CH₄ release → Runaway greenhouse effect ​ Increased ocean temperatures → Reduced O₂ solubility → Widespread ocean anoxia ​ CO₂ dissolved in seawater → Ocean acidification → Coral reef collapse ​ Methane release from permafrost → Accelerated global warming ​ SO₂ release → Acid rain → Vegetation loss → Erosion → Habitat destruction ○​ Aftermath ​ Multiple environmental stressors over millions of years ​ Cascading collapse of ecosystems ​ The Paleozoic ended with Earth's most severe extinction event ​ Mesozoic (252–66 Ma): Age of the Reptiles ○​ Breakup of Pangaea ​ Early Atlantic Ocean formed ​ Continents began shifting toward modern positions ○​ Dominant Species Groups ​ Corals → Scleractinian corals replaced earlier types ​ Dinosaurs → Ranged from small, agile forms to massive herbivores and carnivores ​ Marine Reptiles → Ichthyosaurs, plesiosaurs, and mosasaurs ​ Flying Vertebrates → First powered fliers (Pterosaurs)  ​ Reptiles → Early crocodilians and lizards ​ Birds → Early species like Archaeopteryx ​ Mammals → Small, nocturnal species ​ Plants → ​ Gymnosperms → Conifers, cycads, and ginkgos ​ Angiosperms → Coevolved with pollinators ​ Cenozoic (66 Ma–Today) – Age of the Mammals ○​ Periods: ​ Paleogene (66–23 Ma) ​ Mammals rapidly diversified after dinosaur extinction ​ Neogene (23–2.6 Ma) ​ Modern mammal families emerged ​ Modern bird families emerged ​ Grasses spread ​ Early hominin ancestors appeared ​ Quaternary (2.6 Ma–Present) ​ Ice Ages → Alternating glacial and interglacial periods, last ending ~11,700 years ago ​ Humans rose, agriculture began, and civilizations formed Developmental Changes and Evolution ​ Allometric growth (rate): ○​ Evolutionary change in the rate of developmental events; large morphological differences arise from genes altering growth rates. ​ Heterochrony (timing): ○​ Evolutionary change in the timing of developmental events; large morphological differences arise from genes that control when certain traits are activated. ​ Paedomorphosis: Retention of juvenile traits in adulthood. ​ Gene sequence (spatial): ○​ Hox genes regulate development along the head-to-tail axis of the embryo. Different Hox genes control the development of specific areas. Chapter 26: Phylogeny Phylogeny and the Tree of Life ​ Central Goal ○​ Organize and understand biological diversity. ​ Carolus Linnaeus (1707-1778) ○​ Aimed to comprehend God’s design in nature. ○​ Developed a hierarchical classification system (binomial nomenclature). ○​ Introduced Systema Naturae to classify life into a nested system. ​ Taxonomy ○​ Identification, naming, and hierarchical classification of species. ○​ Initially based on morphological similarity, not evolutionary relationships. ○​ Modern classification incorporates evolutionary relationships. *Memorize: Domain → Kingdom → Phylum → Class → Order → Family → Genus → Species ​ Phylogenetic Groupings ○​ Paraphyletic Group: Includes a common ancestor but not all of its descendants. ​ Incomplete as it excludes certain lineages. ○​ Monophyletic Group: Includes a common ancestor and all its descendants. ​ Represents a true evolutionary lineage. ​ Systematics ○​ Focuses on classifying organisms based on evolutionary relationships (phylogeny). ○​ Phylogenetic Tree: A hypothesis of evolutionary relationships. ​ Based on morphological and molecular homologies (shared ancestry and derived characteristics). ​ Differs from analogies, which result from convergent evolution. ​ Cladistics ○​ Groups organisms by shared derived characteristics. ○​ Clade: Ancestor + all its descendants. ○​ Cladogram: Shows relationships but not time. ○​ Phylogram: Branch lengths reflect evolutionary time. ​ Types of Phylogenetic Trees ○​ Cladogram: Time-independent, only shows branching order. ○​ Phylogram: Time-dependent, branch lengths indicate evolutionary time. ​ Principle of Maximum Parsimony ○​ The simplest explanation (fewest evolutionary changes) is most likely correct.