CHAPTER 26: Phylogeny and the Tree of Life

Learning Objectives

This chapter introduces the concept of phylogeny, the methods used to infer evolutionary relationships, and the structure of the tree of life. Students will learn to differentiate between derived and ancestral characters, understand the evidence genomes provide about evolutionary history, and explain the use of molecular clocks.

• Define phylogeny and explain how phylogenies are determined.

• Explain how phylogenetic trees are inferred from data.

• Differentiate between derived and ancestral characters and explain their use in constructing phylogenies.

• Describe genomic evidence for evolutionary history.

• Explain molecular clocks and their application.

• Describe the structure of the tree of all life and recent changes in classification.

Investigating the Tree of Life

Phylogeny and Systematics

Phylogeny is the evolutionary history of a species or group of related species. The discipline of systematics classifies organisms and determines their evolutionary relationships.

• Phylogenetic tree: Diagram showing evolutionary relationships among species.

• Example: Legless lizards and snakes evolved from lizards with limbs, as shown in a phylogenetic tree.

Binomial Nomenclature and Hierarchical Classification

Developed by Carl Linnaeus in the 18th century, binomial nomenclature assigns each species a two-part scientific name: the genus and the specific epithet.

• Genus: First part, capitalized (e.g., Panthera).

• Specific epithet: Second part, unique for each species (e.g., pardus).

• Hierarchical classification: Species are grouped into increasingly broad categories: Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

Phylogenetic Trees: Interpretation and Limitations

Phylogenetic trees represent hypotheses about evolutionary relationships. Each branch point (node) indicates divergence from a common ancestor.

• Branching pattern: Shows relationships, not exact times of divergence.

• Rotation: Branches can be rotated without changing relationships.

• Tree forms: Trees can be drawn vertically, horizontally, or diagonally.

• Limitation: Trees do not indicate when species evolved or how much genetic change occurred.

Inferring Phylogenies

Morphological and Molecular Data

Systematists use morphological (physical traits) and molecular (DNA, RNA, protein sequences) data to infer phylogenies.

• Homology: Similarity due to shared ancestry.

• Analogy: Similarity due to convergent evolution, not common ancestry.

• Convergent evolution: Independent evolution of similar features in different lineages.

Cladistics and Clades

Cladistics groups organisms by common ancestry. A clade includes an ancestor and all its descendants.

• Monophyletic group: Consists of an ancestor and all its descendants.

• Paraphyletic group: Consists of an ancestor and some, but not all, descendants.

• Polyphyletic group: Includes distantly related species but not their common ancestor.

Shared Ancestral vs. Shared Derived Characters

Characters are used to construct phylogenetic trees.

• Shared ancestral character: Originated in an ancestor of the group.

• Shared derived character: Unique to a particular clade.

• Outgroup: Species or group closely related to the ingroup but not part of it; used to differentiate ancestral and derived characters.

Tree Construction Methods

Maximum Parsimony and Maximum Likelihood

Systematists use principles to narrow down possible trees.

• Maximum parsimony: The simplest explanation (fewest evolutionary changes) is preferred.

• Maximum likelihood: Based on probability rules about how DNA changes over time.

Phylogenetic Trees as Hypotheses

Phylogenetic trees are hypotheses that fit the available data. Phylogenetic bracketing allows prediction of features in extinct organisms based on shared features in living relatives.

• Example: Birds and crocodiles share features likely present in their common ancestor.

Genomic Evidence and Molecular Clocks

Genome Analysis

Comparing nucleic acids or other molecules helps determine evolutionary relationships.

• rRNA genes: Change slowly, useful for deep evolutionary relationships.

• mtDNA: Evolves rapidly, useful for recent divergences.

Gene Duplications and Gene Families

• Orthologous genes: Found in different species, derived from a common ancestor.

• Paralogous genes: Found within a species, resulting from gene duplication.

Molecular Clocks

Molecular clocks use constant rates of evolution in genes to estimate evolutionary time.

• Orthologous genes: Nucleotide substitutions are proportional to time since divergence.

• Paralogous genes: Nucleotide substitutions are proportional to time since duplication.

• Calibration: Molecular clocks are calibrated using fossil record dates.

Equation:

Classification Systems and the Tree of Life

Three-Domain System

Modern classification recognizes three domains: Bacteria, Archaea, and Eukarya.

• Bacteria: Prokaryotic, diverse group.

• Archaea: Prokaryotic, often found in extreme environments.

• Eukarya: Includes all eukaryotic organisms (plants, animals, fungi, protists).

Horizontal Gene Transfer

Horizontal gene transfer is the movement of genes between organisms by mechanisms other than descent from parent to offspring.

• Mechanisms: Exchange of plasmids, transposable elements, viral infection.

• Impact: Has played a key role in the evolution of prokaryotes and eukaryotes.

Summary Table: Types of Groups in Phylogenetics

Key Terms

• Phylogeny

• Systematics

• Clade

• Homology

• Analogy

• Maximum parsimony

• Maximum likelihood

• Orthologous gene

• Paralogous gene

• Molecular clock

• Horizontal gene transfer

Additional info: These notes expand on the brief points and images provided in the original materials, adding definitions, examples, and academic context for clarity and completeness.