🔬General Biology I Unit 20 – Phylogenies and the History of Life

What's This Unit All About?

• Explores the diversity and evolutionary history of life on Earth
• Introduces phylogenies, branching diagrams that depict evolutionary relationships among organisms
• Examines how phylogenetic trees are constructed using morphological, biochemical, and genetic data
• Highlights key events in the history of life, including the origin of life, the evolution of eukaryotic cells, and mass extinction events
• Discusses how phylogenies reveal patterns of evolutionary change and help us understand the relationships between species
• Covers practical applications of phylogenetics in fields such as conservation biology, medicine, and agriculture
• Emphasizes the importance of understanding the tree of life for gaining insights into the unity and diversity of life on our planet

Key Concepts and Definitions

• Phylogeny: a branching diagram that represents the evolutionary relationships among organisms or groups of organisms
• Cladistics: a method of classifying organisms into groups (clades) based on shared derived characteristics
• Synapomorphy: a shared derived character state that is unique to a particular clade and indicates a common ancestor
• Plesiomorphy: an ancestral character state that is shared by multiple clades but does not indicate a common ancestor
• Homology: similarity between structures or DNA sequences that is due to common ancestry
• Analogy: similarity between structures that is due to convergent evolution rather than common ancestry
• Monophyletic group: a group of organisms that includes an ancestor and all of its descendants (a complete clade)

The Tree of Life: Understanding Phylogenies

• Phylogenetic trees depict the evolutionary relationships among organisms, with each branch representing a lineage
• The branching pattern of a phylogeny reflects the sequence of evolutionary events that gave rise to the diversity of life
• Phylogenies can be rooted or unrooted, depending on whether the position of the common ancestor is known
  • Rooted trees have a specific node designated as the common ancestor of all the taxa included in the tree
  • Unrooted trees show the relative relationships among taxa without specifying the position of the common ancestor
• The tips of the branches in a phylogeny represent the present-day taxa (species or higher-level groups)
• The nodes in a phylogeny represent the inferred common ancestors of the descendant lineages
• Branch lengths in a phylogeny can indicate the amount of evolutionary change or time that has elapsed along each lineage
• Phylogenies provide a framework for understanding the evolutionary history and relationships of life on Earth

How We Build Phylogenetic Trees

• Phylogenetic trees are constructed using various types of data, including morphological, biochemical, and genetic evidence
• Morphological data involves comparing the physical characteristics of organisms, such as skeletal structures or leaf shapes
• Biochemical data includes comparing the amino acid sequences of proteins or the structure of other biomolecules
• Genetic data involves comparing DNA sequences, which provide the most direct evidence of evolutionary relationships
• The choice of data depends on the organisms being studied and the specific research question
• Computational methods, such as maximum parsimony and maximum likelihood, are used to infer the most probable tree based on the available data
  • Maximum parsimony seeks the tree that requires the fewest evolutionary changes to explain the observed data
  • Maximum likelihood identifies the tree that is most likely to have produced the observed data given a specific evolutionary model
• Building accurate phylogenetic trees requires careful data collection, rigorous analysis, and an understanding of the assumptions and limitations of different methods

Major Events in Life's History

• The origin of life: The first living organisms emerged on Earth around 3.5-3.8 billion years ago, likely in the form of simple, single-celled prokaryotes
• The evolution of eukaryotic cells: Eukaryotic cells, which have a nucleus and other membrane-bound organelles, evolved around 2.1 billion years ago through endosymbiosis
• The rise of multicellularity: Multicellular organisms evolved independently in several lineages, including animals, plants, and fungi, starting around 1.5 billion years ago
• The Cambrian explosion: A rapid diversification of animal life occurred around 541 million years ago, giving rise to most of the major animal phyla
• The colonization of land: Plants, fungi, and animals began to colonize terrestrial environments around 500-450 million years ago, leading to the development of complex terrestrial ecosystems
• Mass extinction events: Several major extinction events have punctuated the history of life, including the End-Permian (252 million years ago) and the End-Cretaceous (66 million years ago) extinctions, which led to the disappearance of many lineages and the rise of new dominant groups

Evolutionary Relationships Revealed

• Phylogenies reveal the evolutionary relationships among organisms, allowing us to trace the history of life and understand the connections between species
• Closely related organisms share more recent common ancestors and tend to have more similar characteristics
• Phylogenies can help identify instances of convergent evolution, where similar traits evolve independently in distantly related lineages due to similar selective pressures
• Comparing phylogenies based on different types of data (morphology, biochemistry, genetics) can provide a more comprehensive understanding of evolutionary relationships
• Phylogenies can reveal unexpected evolutionary relationships, such as the close relationship between birds and crocodiles within the archosaur lineage
• Studying the evolutionary relationships among organisms can shed light on the mechanisms and patterns of evolutionary change, such as the role of adaptation, speciation, and extinction in shaping the diversity of life

Practical Applications of Phylogenies

• Conservation biology: Phylogenies can inform conservation efforts by identifying evolutionarily distinct lineages that may require special protection
• Medicine: Understanding the evolutionary relationships among pathogens can aid in the development of targeted therapies and predict the emergence of drug resistance
• Agriculture: Phylogenetic analysis can help identify wild relatives of crop plants that may harbor useful traits for breeding and genetic improvement
• Forensics: Phylogenetic methods can be used to trace the origin and spread of infectious diseases or to identify the source of biological materials in criminal investigations
• Bioprospecting: Phylogenies can guide the search for novel compounds or biomolecules from diverse organisms for use in biotechnology and drug discovery
• Evolutionary psychology: Phylogenetic comparisons can provide insights into the evolutionary origins of human behaviors and cognitive abilities
• Astrobiology: Understanding the phylogenetic relationships among Earth's life forms can inform the search for life on other planets and help predict the potential characteristics of extraterrestrial life

Cool Facts and Mind-Blowing Stuff

• The mitochondria in eukaryotic cells are descended from ancient bacteria that were engulfed by a larger cell, establishing an endosymbiotic relationship that has persisted for billions of years
• The closest living relatives of whales and dolphins are hippopotamuses, despite their drastically different appearances and lifestyles
• The extinct Tyrannosaurus rex is more closely related to modern birds than it is to other reptiles like lizards and crocodiles
• Some species of fungi have evolved the ability to control the behavior of insects, turning them into "zombies" that help spread the fungus to new hosts
• The Hawaiian silversword plants, known for their striking rosette shape and silvery leaves, are actually closely related to sunflowers and daisies, having evolved their unique adaptations after colonizing the Hawaiian Islands
• The genome of the extinct woolly mammoth has been sequenced using DNA extracted from frozen tissue, opening up the possibility of using phylogenetic information to guide efforts in de-extinction and species restoration
• Horizontal gene transfer, the exchange of genetic material between distantly related species, has played a significant role in bacterial evolution and the spread of antibiotic resistance
• The evolutionary history of life on Earth has been marked by several mass extinction events, some of which wiped out over 90% of all species, but life has always managed to recover and diversify in the aftermath of these catastrophic events