🐾General Biology II Unit 14 – Phylogeny and the Tree of Life

What's This Unit All About?

• Explores the evolutionary relationships among organisms and how they are represented in phylogenetic trees
• Focuses on the methods used to construct and interpret phylogenetic trees based on molecular and morphological data
• Examines the historical background of phylogenetic analysis, including the contributions of key figures like Charles Darwin and Willi Hennig
• Delves into the different types of phylogenetic trees (rooted, unrooted, cladograms, phylograms) and their specific uses
• Discusses how phylogenetic analysis informs our understanding of evolutionary relationships and the classification of organisms
• Highlights real-world applications of phylogenetic analysis in fields such as conservation biology, epidemiology, and drug discovery

Key Concepts and Definitions

• Phylogeny: the evolutionary history and relationships among organisms or groups of organisms
• Cladistics: a method of classifying organisms based on shared derived characteristics (synapomorphies)
• Monophyletic group (clade): a group of organisms that includes an ancestor and all of its descendants
• Paraphyletic group: a group of organisms that includes an ancestor but not all of its descendants
• Polyphyletic group: a group of organisms that does not include the most recent common ancestor of all the members
• Homology: similarity between characteristics of different organisms due to shared ancestry
• Homoplasy: similarity between characteristics of different organisms due to convergent evolution rather than shared ancestry
  • Includes analogous structures (similar function but different evolutionary origins) and homoplasious traits

Historical Background

• Charles Darwin's theory of evolution by natural selection laid the groundwork for understanding the relationships among organisms
• Willi Hennig developed the principles of cladistics in the 1950s, emphasizing the use of shared derived characteristics to establish evolutionary relationships
• The development of molecular biology techniques (DNA sequencing, PCR) in the late 20th century revolutionized phylogenetic analysis
• Advances in computational power and algorithms have enabled the analysis of large datasets and the construction of complex phylogenetic trees
• The integration of morphological and molecular data has improved the resolution and accuracy of phylogenetic reconstructions

Methods of Phylogenetic Analysis

• Parsimony: selects the phylogenetic tree that requires the fewest evolutionary changes to explain the observed data
• Maximum likelihood: identifies the phylogenetic tree that is most likely to have given rise to the observed data based on a specific evolutionary model
• Bayesian inference: uses prior probabilities and likelihood functions to estimate the posterior probabilities of different phylogenetic trees
• Distance-based methods (UPGMA, neighbor-joining): construct phylogenetic trees based on pairwise distances between sequences or characters
• Molecular clock analysis: estimates the timing of evolutionary events based on the assumption of a constant rate of molecular evolution

Reading and Interpreting Phylogenetic Trees

• Branches represent evolutionary lineages, and nodes represent common ancestors or speciation events
• Branch lengths can indicate the amount of evolutionary change (phylograms) or the passage of time (chronograms)
• Monophyletic groups (clades) are identified by a single common ancestor and all its descendants
• Outgroup: a taxon that is known to be less closely related to the group of interest than any other taxa in the analysis
  • Used to root the tree and determine the direction of evolutionary change
• Bootstrap values or posterior probabilities indicate the level of support for specific clades or branches

Types of Phylogenetic Trees

• Rooted trees: have a specified outgroup and show the direction of evolutionary change
  • Useful for inferring ancestral states and the order of evolutionary events
• Unrooted trees: do not specify the direction of evolutionary change and do not require an outgroup
  • Useful for visualizing the relative relationships among taxa without making assumptions about the root
• Cladograms: show the branching pattern of evolutionary relationships without indicating the amount of evolutionary change or time
• Phylograms: show the branching pattern of evolutionary relationships with branch lengths proportional to the amount of evolutionary change
• Chronograms: show the branching pattern of evolutionary relationships with branch lengths proportional to time

Evolutionary Relationships and Classification

• Phylogenetic analysis reveals the evolutionary relationships among organisms and helps to establish a natural classification system
• Monophyletic groups (clades) are the basis for taxonomic classification at various levels (species, genera, families, orders, etc.)
• Paraphyletic and polyphyletic groups are not considered valid taxonomic units in a phylogenetic context
• Phylogenetic nomenclature (PhyloCode) aims to name clades based on their evolutionary relationships rather than traditional Linnaean ranks
• Convergent evolution can lead to similar morphological features in distantly related organisms, emphasizing the importance of molecular data in phylogenetic analysis

Real-World Applications and Case Studies

• Conservation biology: phylogenetic diversity is used to prioritize species and areas for conservation efforts
  • Helps to identify evolutionarily distinct and globally endangered (EDGE) species
• Epidemiology: phylogenetic analysis is used to trace the origin and spread of infectious diseases (HIV, influenza, SARS-CoV-2)
  • Informs public health strategies and vaccine development
• Drug discovery: phylogenetic analysis can identify evolutionarily conserved drug targets and predict potential side effects
  • Helps to streamline the drug discovery process and reduce the risk of adverse reactions
• Comparative genomics: phylogenetic analysis is used to study the evolution of genomes and identify functionally important regions
  • Contributes to our understanding of the genetic basis of adaptations and diseases
• Forensic science: phylogenetic analysis can be used to identify the source of biological evidence (plant fragments, animal hairs) in criminal investigations