11-15 Origins and evolution
Page 1: Introduction
Title: Origins and evolution
Instructor: Dr. Mitchell Balish
Course: MBI 201
Date: 11/15/24
Page 2: Chapter Overview
Topics Covered:
Forming the first cells
Evolution: Phylogeny and Gene Transfer
Natural Selection and Adaptation
Microbial Species and Taxonomy
Page 3: Forming the First Cells
Key Questions:
Environment of early cells?
Metabolism used for energy generation?
Hereditary material of first cells?
Page 4: The Prebiotic Soup
Evidence:
Small organic molecules formed abiotically from simple chemicals triggered by lightning.
Further reactions led to complex macromolecules capable of self-replication and membrane compartmentalization.
Page 5: Early Oxidation-Reduction Reactions
Oxygen Levels:
Early Earth had no free oxygen; photosynthesis was undeveloped.
Energy Generation:
Abiotically produced oxidized minerals reacted with hydrogen gas.
Photoferrotrophy: Nutrient process used by bacteria to gain energy from light by oxidizing Fe2+ to Fe3+.
Process powers carbon fixation in bacteria.
Page 6: The RNA World
RNA's Role:
RNA replaced DNA and proteins in early life for information encoding and catalytic functions.
Advantages of RNA:
Requires less energy for construction and degradation.
Ribozymes:
Catalytic RNA molecules revealing how RNA may have fulfilled key biochemical functions in early cells.
Page 7: Unresolved Questions about Early Life
Evidence suggests early organisms resembling cyanobacteria existed 2.5–3.7 billion years ago, some anaerobic bacteria potentially dating back to 4.2 billion years.
Key Questions:
What was the temperature of early Earth?
Source of Earth’s first cells?
Page 8: Evolution: Phylogeny and Gene Transfer
Clades:
Groups of related organisms sharing a common ancestor; monophyletic groups.
Phylogeny:
The full description of branching divergences within species.
Page 9: Divergence through Mutation and Natural Selection
Mechanisms of Evolution:
Random mutations occurring during chromosome replication.
Natural selection aligning with adaptation to favor offspring production.
Reductive Evolution: Loss of unselected traits through mutation.
Page 10: Molecular Clocks
Concept:
Molecular clocks provide temporal measures based on mutation accumulation rates during DNA replication.
Page 11: Molecular Clocks Characteristics
Reliable Genes:
Genes encoding transcription and translation machinery (e.g., ribosomal RNA) used for accurate evolutionary timing.
Commonly Used Genes:
Small subunit rRNA genes (16S rRNA in bacteria; 18S rRNA in eukaryotes).
Page 12: Calculating Phylogenetic Trees
Accuracy:
Requires extensive sequence data for higher precision.
Data Analysis:
Computer programs may result in variability based on underlying assumptions.
Page 13: Divergence of Three Domains of Life
Carl Woese's Contribution:
Established three life domains: Bacteria, Archaea, and Eukarya.
Evolutionary Insights:
Shared similarities across all living cells while highlighting significant domain differences.
Page 14: Three Domains of Life - Characteristics Table
Characteristics:
Bacteria: Circular DNA, nucleoid organization, lacks introns.
Archaea: Circular DNA, nucleoid organization, more frequent introns.
Eukarya: Linear DNA, organized in a nucleus, possesses introns.
Page 15: Three Domains of Life - Continued
Verifiable Differences:
Variability in ribosome sensitivity and metabolic processes (e.g., methanogenesis).
Page 16: Horizontal Gene Transfer
Definitions:
Horizontal Gene Transfer: Acquisition of DNA from another cell.
Vertical Gene Transfer: Genome transmission from parent to offspring.
Mechanisms:
Horizontal transfer facilitated by plasmids, transposable elements, and bacteriophages.
Page 17: Vertical and Horizontal Gene Transfer
Traditional View:
Majority of gene transfer is vertical; organisms typically exhibit monophyletic lineage.
Alternative View:
Horizontal transfer prevalent in microbes disrupts traditional monophyletic classifications.
Page 18: Reconciling Gene Transfer Types
Informational vs. Operational Genes:
Informational Genes: Crucial for fundamental processes; less likely to transfer horizontally.
Operational Genes: Govern metabolism and response, often transmitted horizontally.
Page 19: Balanced Views in Gene Transfer
Visualization:
The model illustrates directionality of both vertical and horizontal gene transfers as distinct.
Page 20: Natural Selection and Adaptation
Evolutionary Mechanisms:
Natural selection among surviving variants shapes adaptations to new environments.
Page 21: Genomic Analysis
Utility:
Gene sequence comparison reveals insights into historical adaptations and evolution.
Gene Duplications:
Allow development of paralogs with diverse functions.
Page 22: Strongly Selective Environments
Examples:
Antibiotic resistance in MRSA illustrates adaptive evolution under selective stress.
Key Points:
Environmental factors dictate the beneficial traits influencing fitness.
Page 23: Experimental Evolution in the Lab
Methodology:
Laboratory experiments track evolution using controlled environmental conditions.
Page 24: Landmark Experiment by Richard Lenski
Long-Term Evolution Experiment (LTEE):
Began in 1988 with 12 cloned E. coli populations, culturing under glucose-limited conditions.
Storage and Continuation:
Population samples preserved for later genetic analysis.
Page 25: Observing Evolutionary Changes
Significant Findings:
Evolution of E. coli with enhanced growth capabilities (Cit+ phenotype) observed at generation 33,000.
Page 26: Staged Model of Trait Evolution
Evolutionary Model Stages:
Potentiation (useful mutations)
Actualization (novel phenotypes)
Refinement (enhanced expression of traits)
Page 27: Mechanism of Citrate Utilization
Mutation Result:
Inhibition of NADH in citrate production allows anaerobic growth as glucose depletes.
Page 28: Microbial Species and Taxonomy
Species Definition in Prokaryotes:
Defined less traditionally due to asexual reproduction; significant debate exists in classification systems.
Page 29: Defining a Microbial Species
Quantitative Divergence Analysis:
Genetic sequence divergence as a basis for defining microbial species proves complex.
Agreed Perspectives:
Phylogenetic analysis based on DNA and ecological similarities are crucial for classification.
Page 30: Working Definition of Species
Criteria for Classification:
SSU rRNA similarity ≥95%
Average nucleotide identity (ANI) ≥95%
Shared ecotype reflects environmental niches.
Page 31: Nongenetic Categorization Systems
Categories of Practical Use:
Phenotypic: Identifiers like Gram-positive rods.
Ecological: Grouping based on ecological roles.
Disease-Based: Classifying by infection type.
Page 32: Naming Species Protocol
Establishment:
New species founded on isolating and cultivating previously unknown microbes.
Official names published following isolation and identification standards by the ICSP.
Page 33: Summary of Key Concepts
Early Metabolism: Characterized by anaerobic oxidation-reduction.
Molecular Clocks: Utilized to measure evolutionary timelines based on mutation rates.
Phylogenetic Trees: Created via sequence similarity of organisms.
Three Domains of Life: Recognizable divergence into Bacteria, Archaea, and Eukarya.
Gene Transfer Types: Both horizontal and vertical impact lineage classification.
Adaptive Evolution: Requires natural selection, supported by genomic analysis and experiments.
Microbial Species: Defined by genomic characteristics in conjunction with ecological functions.