Exam 1 Lecture: Evolutionary Biology: Chapters 21–26 Study Guide

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Chapter 21: Genomes and Their Evolution (pp. 444–458)

The Human Genome & Bioinformatics

The Human Genome Project (HGP) revolutionized our understanding of genome structure and function, providing a foundation for modern bioinformatics and comparative genomics.

Genome: The complete set of genetic instructions for an organism.
Scale: Human cells contain 46 chromosomes, about 3 billion nucleotide pairs, and roughly 20,000–30,000 protein-coding genes.
Bioinformatics: The use of computational tools to analyze and interpret biological data, especially large-scale genomic datasets.
Gene Density: Eukaryotes, especially mammals, have lower gene density than prokaryotes due to large amounts of noncoding DNA.

Genomic Composition

Most of the human genome does not code for proteins. Understanding the composition of the genome is essential for interpreting genetic function and evolution.

Exons (1.5%): Protein-coding regions.
Regulatory Sequences (5%): Control gene expression.
Introns (20%): Noncoding regions within genes, removed during RNA processing.
Unique Non-coding DNA (15%): Includes pseudogenes (nonfunctional gene remnants).
Repetitive DNA (14%): Simple sequence repeats and large-segment duplications.
Transposable Elements (44%): Mobile DNA sequences, including L1 (17%) and Alu (10%) elements.

Transposable Elements

Transposable elements, or "jumping genes," are major contributors to genome evolution and diversity.

Transposons: Move via DNA intermediates using transposase ("cut-and-paste" or "copy-and-paste").
Retrotransposons: Move via RNA intermediates, requiring reverse transcriptase ("copy-and-paste").

Mechanisms of Genetic Variation

Genetic variation is the foundation of evolutionary change. Mutations and chromosomal alterations generate new alleles and gene combinations.

Point Mutations: Single nucleotide changes, including silent, missense, and nonsense mutations.
Insertions/Deletions: Can cause frameshift mutations, altering the reading frame of genes.
Mutation of Regulatory Sequences: Can alter gene expression levels.

Creation of New Genes & Multigene Families

Gene Duplication: Unequal crossing over during meiosis can create extra gene copies, which may evolve new functions.
Exon Shuffling: Mixing of exons between genes, creating proteins with novel domains.
Multigene Families: Groups of related genes, such as the globin gene family, arising from duplication and divergence.

Chromosomal Alterations

Polyploidy: Whole-genome duplication, common in plants, can lead to speciation.
Chromosome Fusion: Example: Human chromosome 2 formed by fusion of two ancestral chromosomes.
Inversions: Chromosome segments break, flip, and reattach, altering gene order.
Homologous Recombination: Exchange of DNA segments during meiosis, increasing genetic diversity.

Evolutionary Development (Evo-Devo) & Hox Genes

Homeotic (Hox) Genes: Master regulatory genes controlling body plan development; contain a conserved homeobox sequence.
Colinearity: The order of Hox genes on the chromosome matches their expression pattern along the body axis.
Vertebrate Evolution: Two rounds of Hox gene cluster duplication contributed to vertebrate complexity.

Case Studies

Stickleback Fish: Loss of pelvic spines in lake populations due to regulatory mutations.
Lizard Adaptive Radiation: Independent evolution of similar ecomorphs on different islands.
Insect Evolution: Ubx gene changes led to reduction in leg number from crustacean ancestors.

Chapter 22: Descent with Modification—A Darwinian View of Life

The Roots of Evolutionary Thought

Early scientists laid the groundwork for evolutionary theory, though their mechanisms were often incorrect.

Aristotle: Species are fixed; arranged on a scala naturae.
Linnaeus: Developed binomial nomenclature; grouped species by similarity.
Cuvier: Founded paleontology; advocated catastrophism.
Hutton & Lyell: Proposed gradualism and uniformitarianism, providing the concept of "deep time."
Lamarck: Proposed use/disuse and inheritance of acquired traits (mechanism incorrect, but recognized adaptation).

Darwin’s Observations & Inferences

Observation 1: Inherited variation exists within populations.
Observation 2: Species produce more offspring than the environment can support.
Inference 1: Individuals with advantageous traits leave more offspring.
Inference 2: Favorable traits accumulate over generations (adaptation).

Core Concepts of Evolution

Evolution: Descent with modification.
Unit of Evolution: Populations evolve, not individuals.
Natural Selection: Edits existing variation; context-dependent; can lead to speciation.

Pillars of Evidence for Evolution

Direct Observation: Soapberry bug beak size, antibiotic resistance, peppered moth color shifts.
Artificial Selection: Domestication of plants and animals.
Anatomical Structures:
- Homologous Structures: Common ancestry (e.g., mammalian forelimbs).
- Analogous Structures: Convergent evolution (e.g., sugar glider and flying squirrel).
Fossil Record: Transitional forms, radiometric dating, cetacean origins.
Biogeography: Continental drift, snapping shrimp speciation.
Molecular Biology: Shared genetic code, DNA/protein homology (e.g., human-chimpanzee 99% identity).

Feature	Divergent Evolution	Convergent Evolution
Origin	Common Ancestor	Different Ancestors
Structures	Homologous	Analogous
Result	Species become more different	Unrelated species look similar
Example	Human arm / Bat wing	Sugar glider / Flying squirrel

Chapter 23: The Evolution of Populations

Foundations of Microevolution

Microevolution: Change in allele frequencies within populations over time.
Genetic Variation: Heritable differences among individuals; the substrate for evolution.
Phenotypic Variation:
- Discrete Characters: Distinct categories (e.g., flower color).
- Continuous Characters: Range of values (e.g., height).

Sources of Genetic Variation

Mutation: Creates new alleles.
Rapid Reproduction: Increases mutation spread (notably in bacteria).
Sexual Reproduction: Shuffles alleles via crossing over, independent assortment, and fertilization.

Measuring Genetic Variation

Gene Variability: Average heterozygosity in a population.
Nucleotide Variability: Percent difference in DNA sequences among individuals.

Hardy-Weinberg Equilibrium

Describes a non-evolving population. Five conditions must be met:

No mutations
Random mating
Large population size
No gene flow
No natural selection

Equations:

Allele frequency:
Genotype frequency:

Causes of Changes in Allele Frequency

Genetic Drift: Random changes, especially in small populations (founder effect, bottleneck effect).
Gene Flow: Movement of alleles between populations.
Natural Selection: Only mechanism that consistently leads to adaptation.

Types of Selection

Directional Selection: Favors one extreme phenotype.
Disruptive Selection: Favors both extremes.
Stabilizing Selection: Favors intermediate phenotypes.

Sexual Selection

Sexual Dimorphism: Differences between sexes in traits.
Intrasexual Selection: Competition among one sex (often males).
Intersexual Selection: Mate choice (often female choice).

Preserving Genetic Variation

Diploidy: Recessive alleles can persist in heterozygotes.
Balancing Selection: Maintains multiple alleles (heterozygote advantage, frequency-dependent selection).

Chapter 24: The Origin of Species

Evolutionary Scales & The Origin of Species

Microevolution: Changes within a population.
Macroevolution: Broad patterns above the species level.
Speciation: Formation of new species.

Defining a Species

Biological Species Concept: Groups of interbreeding populations reproductively isolated from others.
Morphological, Phylogenetic, Ecological Species Concepts: Based on structure, ancestry, or ecological niche.

Reproductive Isolation

Pre-zygotic Barriers: Prevent fertilization (habitat, temporal, behavioral, mechanical, gametic isolation).
Post-zygotic Barriers: Prevent hybrid viability or fertility (reduced viability, reduced fertility, hybrid breakdown).

Mechanisms of Speciation

Allopatric Speciation: Geographic separation leads to divergence.
Sympatric Speciation: Speciation without geographic separation (habitat differentiation, sexual selection, polyploidy).

Hybrid Zones & Outcomes

Reinforcement: Strengthening of reproductive barriers.
Fusion: Weakening of barriers; species merge.
Stabilization: Continued production of hybrids.

Chapter 25: The History of Life on Earth (Review)

Key Events in the History of Life

Urey and Miller Experiment: Simulated early Earth conditions, producing amino acids from inorganic molecules.
RNA World Hypothesis: RNA can act as a catalyst, self-replicate, and adopt diverse shapes, making it a likely first genetic molecule.
Protobionts: Aggregates of abiotically produced molecules surrounded by a membrane; precursors to living cells.
Fossils & Carbon-14 Dating: Fossils provide evidence of ancient life; C half-life is about 5,730 years.
Oxygen Revolution: Cyanobacteria produced oxygen, transforming Earth's atmosphere.
Endosymbiosis: Mitochondria evolved from proteobacteria; chloroplasts from cyanobacteria. Evidence includes double membranes and their own DNA.
Geological Time: Three eons (Archaean, Proterozoic, Phanerozoic); Phanerozoic divided into Paleozoic, Mesozoic, Cenozoic eras.
Mass Extinctions: Permian and Cretaceous periods; caused by volcanic activity, asteroid impact, etc.
Adaptive Radiation: Rapid diversification following mass extinctions or new ecological opportunities.
Pangea & Plate Tectonics: Continental drift reshaped habitats and drove speciation.
Paedomorphosis & Heterochrony: Evolutionary changes in the timing of developmental events.

Chapter 26: Phylogeny and the Tree of Life

Phylogeny and Systematics

Phylogeny: Evolutionary history of a species or group.
Systematics: Classification of organisms and determination of their evolutionary relationships.

Cladistics and Cladograms

Cladogram: Diagram showing evolutionary relationships based on shared derived characters.
Shared Derived Character: Trait unique to a particular clade.
Shared Ancestral Character: Trait present in the ancestor of a group.

Types of Clades

Monophyletic: Includes ancestor and all descendants.
Paraphyletic: Includes ancestor and some, but not all, descendants.
Polyphyletic: Includes distantly related species but not their most recent common ancestor.

Principles of Phylogenetic Inference

Maximum Parsimony: The simplest explanation (fewest evolutionary changes) is preferred.
Maximum Likelihood: Considers probability of observed data given certain models of evolution.