BIOL 1407 Chapter 20 - Phylogenies and the History of Life

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Adapted from OpenStax Biology 2e.

Discuss the need for a comprehensive classification system.
List the different levels of the taxonomic classification system.
Describe the relationship between systematics, taxonomy, and phylogeny.
Discuss the components and purpose of a phylogenetic tree.
Explain the purpose of cladistics.
Analyze the role of greenhouse gases in shaping early climate conditions.
Describe how continental drift and tectonic plate movements have shaped Earth’s surface over geological time.
Identify and describe the four main eons of Earth’s history: Hadean, Archean, Proterozoic, and Phanerozoic.
Describe the major evolutionary developments during the Cambrian period.
Analyze the significance of CO₂ and other greenhouse gases in the Miller-Urey experiment setup for simulating early Earth conditions.
Identify key types of fossil evidence indicating early life on Earth.
Explain the causes and consequences of global glaciation events (e.g., Snowball Earth).
Describe the chemical processes that led to the formation of the ozone layer.
Detail the evolutionary steps leading to the development of the endomembrane system in eukaryotic cells.

Relationships between different organisms can be observed through shared characteristics.
Example: A bee's life is related to a flower's, both share the domain Eukarya with similar organelles and processes.

Characteristics of all organisms:
- Composed of one or more cells.
- Carry out metabolism.
- Transfer energy using ATP.
- Encode hereditary information in DNA.
Estimates of biodiversity:
- Cataloged species: 1.5 to 2.3 million
- Total estimated species: 5 million (±3 million)
- Total estimated individuals: 100 billion to 1 trillion (including prokaryotes).

Systematics: Study of evolutionary relationships and classification of organisms.
Phylogeny: Evolutionary history and relationships of organisms depicted in a phylogenetic tree or cladogram.
Comparisons to family trees help visualize these relationships.

Rooted Tree: Indicates a common ancestor; attempts to identify divergence points.
Unrooted Tree: Shows relationships without indicating a common ancestor.

Taxon (taxa, pl): Groups of organisms (species, family, domain).
Clade: A branch or lineage in cladograms.
Branch Point (Node): Indicates a lineage evolving into two clades, representing the most recent common ancestor (MCRA) of the clades.
- Taxa sharing a node share a common ancestor but did not evolve from each other.
- A lineage that remains unbranched is a basal taxon.
- Sister taxa stem from the same branch point.
- Polytomy: A branch with more than two lineages showing unclear relationships.

Multiple biological disciplines contribute to understanding the evolutionary process and maintaining the “tree of life.”
Combining data: Fossil records, body part structures, molecules, and DNA sequence analysis to construct an organism's phylogeny.

Process to arrange taxa based on shared homologous characters into clades (cladograms).
Aim: Produce monophyletic cladograms (holds a single common ancestor and all its descendants).
Monophyletic group: Includes all descendants of a given ancestor.
Paraphyletic group: Includes the most recent common ancestor but not all its descendants.
To accurately develop cladograms, a diverse range of characters should be used to prevent misrepresentation of evolutionary relationships.

Organizes Earth’s 4.6 billion-year history:
- Hierarchy: Eons → Eras → Periods → Epochs → Ages.
- Each division signifies significant historical changes.
Dating Methods:
- Relative dating: Establishes the sequence of historical events.
- Absolute dating: Provides exact ages through methods like radioactive decay.

Hadean Eon (4.6 - 4.0 billion years ago): Earth's formation and early crust; intense meteorite bombardment.
Archean Eon (4.0 - 2.5 billion years ago): Emergence of first life forms and primitive atmosphere; continental development.
Proterozoic Eon (2.5 billion - 541 million years ago): Appearance of multicellular organisms, significant oxygen accumulation, and formation of the supercontinent Rodinia.
Phanerozoic Eon (541 million years ago - present): Visible life forms, explosion of complex life, Pangaea formation and breakup.

Paleozoic Era (541 - 252 million years ago): Origin of hard-shelled organisms, fish, amphibians, early reptiles, formation of Pangaea.
Mesozoic Era (252 - 66 million years ago): Age of dinosaurs; evolution of mammals and birds.
Cenozoic Era (66 million years ago - present): Rise of mammals, modern plants, and human evolution.

Cambrian Period (541-485 million years ago): Rapid evolution of most animal phyla and rich fossil record.
Permian Period (299-252 million years ago): Completion of Pangaea; major mass extinction event at end of Paleozoic Era.
Cretaceous Period (145-66 million years ago): End of dinosaurs' dominance and significant extinction.

Initial Composition: Dominated by volcanic outgassing (water vapor, CO₂, methane, ammonia).
CO₂ levels: Much higher than today (>100,000 ppm), contributing to a strong greenhouse effect.
Absence of Free Oxygen: Early Earth's atmosphere was reducing (oxygen-free), crucial for early chemical evolution.

Conducted by Stanley Miller and Harold Urey in 1952 to simulate early Earth conditions.
Setup:
- Sealed flask of components plus simulated lightning.
- After one week, amino acids were formed.
Findings: Provided evidence that organic compounds may have evolved from inorganic matter supporting the primordial soup hypothesis.

Initially found fossils (~3.5-3.8 billion years ago) are associated with domain Bacteria.
Important findings: Fossil records and genome studies help in understanding evolution and common ancestry.
Ediacaran fauna from 543 - 635 million years ago features organisms believed to be precursors of modern animals.

Mass extinction events can lead to significant biodiversity losses.
Permian-Triassic Boundary: Notable for 95% species extinction (e.g., trilobites), facilitating the emergence of dinosaurs.
Cretaceous-Paleogene Boundary: Led to the extinction of non-avian dinosaurs due to a massive asteroid impact and climate change.
Current concerns indicate a sixth mass extinction driven by human activity, with extinction rates surpassing previous events.

There have been five mass extinction events that dramatically altered Earth’s biological landscape.
Current theories and ongoing studies seek to understand the implications of the sixth mass extinction.