8.7 Phylogeny

Phylogeny is like a family tree for all living things. It shows how different organisms are related and how they evolved over time. Scientists use clues from fossils, DNA, and physical traits to figure out these relationships.

Understanding phylogeny helps us see the big picture of life's history. It shows how species are connected, how new traits appeared, and why some animals look similar even if they're not closely related. This knowledge is key to grasping natural selection.

Phylogeny for Evolutionary Relationships

Defining Phylogeny and Its Role

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• Phylogeny represents the evolutionary history and relationships among groups of organisms
  • Often depicted as branching diagrams called phylogenetic trees
• Phylogenetic trees represent hypotheses about the evolutionary relationships among taxa based on shared derived characters
• Phylogenies are constructed using morphological, biochemical, and genetic evidence to infer common ancestry and divergence among lineages
• Depict the order in which lineages diverged from common ancestors and the relative timing of these divergence events
• Used to understand the evolutionary history of life, trace the origin of traits, and classify organisms based on evolutionary relationships

Applications and Importance of Phylogeny

• Helps in understanding the evolutionary history of life on Earth
  • Traces the origin and diversification of different lineages (animals, plants, fungi)
• Allows for the identification of shared derived characters (synapomorphies) that define monophyletic groups (clades)
• Provides a framework for comparative studies across different taxa
  • Enables the study of character evolution and adaptation (development of flight in birds and bats)
• Informs taxonomy and classification of organisms based on evolutionary relationships rather than superficial similarities
• Contributes to fields such as evolutionary developmental biology (evo-devo) and molecular systematics

Phylogenetic Tree Construction Methods

Character-Based Methods

• Parsimony methods aim to find the tree that requires the fewest evolutionary changes to explain the observed data
  • Assumes that the simplest explanation is the most likely
• Maximum likelihood methods estimate the probability of the observed data given a particular phylogenetic tree and model of evolution
  • Seeks the tree with the highest likelihood
• Bayesian inference incorporates prior knowledge about the probability of different tree topologies
  • Estimates the posterior probability of trees based on the observed data
• Character-based methods use the distribution of character states among taxa to infer evolutionary relationships

Distance-Based Methods

• Distance-based methods use pairwise distances between taxa to construct trees
  • Assumes that more similar sequences are more closely related
• Neighbor-joining is a commonly used distance-based method
  • Starts with a star-like tree and iteratively joins the closest pairs of taxa
• UPGMA (Unweighted Pair Group Method with Arithmetic Mean) is another distance-based method
  • Assumes a constant rate of evolution across all lineages
• Distance-based methods are computationally efficient but may not always recover the true evolutionary relationships

Interpreting Phylogenetic Trees

Tree Topology and Branch Lengths

• The branching pattern of a phylogenetic tree represents the evolutionary relationships among taxa
  • Closely related taxa share more recent common ancestors
• Nodes represent hypothetical common ancestors, while branches represent lineages that have diverged from those ancestors
• Branch lengths can indicate the amount of evolutionary change or time since divergence, depending on the method used
  • Longer branches suggest more evolutionary change or a longer time since divergence
• The arrangement of taxa on a phylogenetic tree does not necessarily reflect their geographic distribution or ecological relationships

Monophyletic, Paraphyletic, and Polyphyletic Groups

• Monophyletic groups (clades) consist of an ancestor and all its descendants
  • Defined by shared derived characters (synapomorphies)
• Paraphyletic groups exclude some descendants of a common ancestor
  • Defined by shared ancestral characters (plesiomorphies)
• Polyphyletic groups include taxa that do not share a recent common ancestor
  • Arise due to convergent evolution or incorrect grouping of taxa
• Outgroup taxa are used to root the tree and determine the direction of evolutionary change
  • Outgroup is more distantly related to the ingroup taxa

Homology, Convergence, and Reversal

• Homologous traits are shared due to common ancestry
  • Can be used to infer evolutionary relationships (forelimbs of mammals)
• Convergent evolution results in similar traits arising independently in distantly related lineages
  • Occurs due to similar selective pressures (wings in birds and bats)
• Evolutionary reversals involve the loss of a derived trait and the reappearance of an ancestral state
  • Can lead to incorrect phylogenetic inferences if not accounted for

Parsimony vs Maximum Likelihood

Parsimony Analysis

• Seeks the tree that requires the fewest evolutionary changes (steps) to explain the distribution of character states among taxa
• The most parsimonious tree is considered the best hypothesis of evolutionary relationships
  • Assumes that evolution tends to follow the simplest path
• Parsimony informative characters exhibit at least two different states and are present in at least two taxa
  • Provide information for inferring relationships
• Parsimony analysis can be sensitive to long-branch attraction
  • Rapidly evolving lineages may be artificially grouped together due to homoplasy (convergence or reversal)

Maximum Likelihood Analysis

• Estimates the probability of the observed data given a tree topology and model of evolution
  • Model includes parameters such as substitution rates and branch lengths
• The likelihood of a tree is the product of the probabilities of each character evolving along the branches of the tree, given the model
• The tree with the highest likelihood is considered the best estimate of the evolutionary relationships among the taxa
  • Given the data and model
• Maximum likelihood can accommodate complex models of evolution and provide statistical support for inferred relationships
• Like parsimony, maximum likelihood can be affected by long-branch attraction and model misspecification