Phylogeny

Expected Learning Outcomes

• Phylogenetic Trees

  • Understand the definition of a monophyletic group/clade

  • Read and interpret phylogenetic tree diagrams

  • Determine the relatedness of taxa

  • Differentiate homologous traits from analogous traits/homoplasies

  • Distinguish between convergent vs. divergent evolution

  • Identify derived vs. ancestral traits

  • Identify synapomorphies

  • Apply the principle of parsimony to phylogenetic trees

Phylogenetic Tree Structure

• Present and Past Relationships

  • Polytomy: indicates uncertainty in relationships

  • Node: represents an ancestral or extinct population, serving as the common ancestor to lineages

  • Branch: stems from a node, indicating evolutionary independence

Key Definitions

• Sister Taxa: groups that emerge from a common ancestor

• Rooted Trees: depend on an outgroup to establish a baseline for the ingroup

Monophyletic Groups

• Defined as a group consisting of a most recent common ancestor and all its descendants

• Example: All members sharing a common ancestor are included in a monophyletic group

Reading Phylogenetic Trees

• Understanding Taxa Relationships:

  • Taxon D is more closely related to taxon E rather than to C

    • Based on the most recent common ancestors at nodes 3 and 4

    • Node 4 is more recent than node 3

Basic Terminology

• Root, Node, Branch, Character Trait

• Ingroup, Outgroup, Sister Taxa, Polytomy

• Pleisiomorphic, Apomorphy, Autapomorphy, Synapomorphy, Monophyletic Group

Clades and Their Traits

• Clades Representing Multicellularity

  • All members are multicellular

  • The shared trait of multicellularity is derived, facilitating group classification

Evolution of Traits

• Derived vs. Ancestral Traits

  • Traits can be classified as pleisiomorphic (ancestral) or apomorphic (derived)

  • Example: Multicellularity is a pleisiomorphy in vertebrates

Advanced Clade Characteristics

• Subsequent clades may also incorporate derived traits:

  • Hinged jaws add specificity to monophyletic groups

  • Shared derived traits are crucial for determining evolutionary relationships

Phylogenetic Analysis and Common Ancestry

• Phylogenies Based on DNA vs Morphology

  • Morphological trees may conflict with those based on DNA

  • Collecting comprehensive data helps clarify relationships and resolve issues like polytomies

Evolutionary Patterns

• Recognizing Homologous vs. Analogous Structures

  • Homologous structures may have similar appearance and function

  • For example, mammalian and frog eyes share homology

Problems in Phylogenetic Construction

• Sources of Uncertainty

  • Incomplete knowledge of common ancestors

  • Independent evolution of similar adaptations (convergent evolution)

  • Loss of evolutionary traits

Homoplasy and Convergence in Evolution

• Similar adaptations may arise through:

  • Convergent Evolution: traits evolve independently under similar selection pressures

  • Example: Fruit fly wings and kiwi bird wings

Non-Monophyletic Groups

• Paraphyletic Groups: excludes some descendants of common ancestors

  • Example: Osteichthyes

• Polyphyletic Groups: includes taxa without a recent common ancestor

  • Example: group based on endothermy in mammals and birds

Building and Assessing Phylogenetic Trees

• Exploring methods of tree construction

  • Parsimony: fewest trait changes as the null hypothesis

  • Maximum Likelihood and Neighbor Joining: alternative assessments of phylogenies

Complexity of Phylogenetic Possibilities

• With increasing taxa, the number of potential phylogenetic trees expands exponentially.