16.4 Molecular Evolution and Phylogenetics

Molecular evolution tracks genetic changes over time, revealing species' histories and relationships. The molecular clock hypothesis helps date evolutionary events, while anagenesis and cladogenesis explain how species change and split.

Phylogenetics uses DNA and protein sequences to build family trees of life. These trees show how species are related, when they split apart, and how they've changed. Different methods help scientists create and check these evolutionary maps.

Molecular Evolution

Molecular clock hypothesis and applications

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• Assumes mutations accumulate at a steady rate over time in a lineage enabling estimation of evolutionary event timing
• Constant molecular evolution rate allows calibration using fossil records (Cambrian explosion) or known events (emergence of land plants) to infer divergence times and ages of common ancestors
• Provides a timeline for speciation events (human-chimpanzee split) and the evolution of lineages (mammalian radiation)

Anagenesis vs cladogenesis in evolution

• Anagenesis: gradual accumulation of mutations and allele frequency changes within a single lineage transforming a species into a new form (Peppered moth industrial melanism)
• Cladogenesis: splitting of lineages through allopatric (geographic isolation) or sympatric (ecological niche differentiation) speciation increasing taxa diversity (Darwin's finches)
• Molecular evolution context: anagenesis involves molecular changes within a lineage while cladogenesis results in divergence of molecular sequences between split lineages (cytochrome c in primates vs rodents)

Phylogenetics

Interpretation of phylogenetic trees

• Branching diagrams depicting evolutionary relationships with nodes representing common ancestors or divergence points and branches indicating lineages
• Branch lengths represent evolutionary time (molecular clock) or genetic change amount (nucleotide substitutions)
• Closely related taxa share a more recent common ancestor (humans and chimpanzees) while sister taxa are each other's closest relatives (lions and tigers)
• Monophyletic groups (clades) include an ancestor and all descendants (mammals) rooted by an outgroup (birds) to determine evolution direction

Methods for phylogenetic tree construction

1. Sequence alignment to identify homologous characters (DNA or protein sequences)
2. Selection of an appropriate evolutionary model (Jukes-Cantor, Kimura 2-parameter)
3. Tree-building algorithms:
   • Maximum parsimony: minimizes the total number of character state changes required to explain the data assuming the simplest explanation is most likely (morphological traits)
   • Maximum likelihood: estimates the probability of the observed data given a tree and evolution model selecting the tree that maximizes the data likelihood (DNA sequences)
   • Neighbor-joining: clusters taxa based on pairwise distances to construct a tree (large datasets)
   • Bayesian inference: calculates the posterior probability of trees based on prior probabilities and the likelihood of the data (complex models)
4. Assessment of tree reliability using bootstrap analysis (resampling) or posterior probabilities (Bayesian inference)