BIO 110: Systematics and Phylogeny

Systematics and Phylogeny

• Systematics and phylogeny are part of BIO 110.
• The study of characteristics and relationships in organisms is discussed.
• Objectives listed for the course include familiarization with characteristics, understanding the relationship between characters and homology, and interpreting phylogenetic trees.

Outline

• Characters:
  • Intrinsic vs extrinsic characters.
  • Genotypic vs phenotypic characters.
• Homology (Homology Assessment):
  • Ontogeny
  • Tokogeny
  • Phylogeny
• Divergent and Convergent:
  • Different species evolving from a common ancestor.
  • Unrelated species developing similar traits due to similar conditions.
• Tree Interpretation:
  • Phylogenetic trees
  • Assumptions about trees

Characters

• Fundamental unit of systematic analysis.
• Theory-laden objects.
• Used for comparison.
• Intrinsic and heritable features are commonly used.
• Character = property/component/feature.

Intrinsic vs Extrinsic

• Intrinsic: morphology, behavior, biochemistry.
• Extrinsic: population size, geographic location, environmental conditions.

Genotypic vs Phenotypic

• Genotypic: most obvious source of comparative variation, all changes are heritable.
• Phenotypic: clearly more similar in parents and offspring, traits like anatomy, behavior, shape, size.

How about Character States?

• States can be: binary (yes/no) or multistate (numerical); quantitative (e.g., weight) or qualitative (e.g., spotted); discrete (e.g., number of legs) or continuous (e.g., weight).
• Character states for specific categories (habit, leaves, inflorescence) are detailed.

Homology

• Similarities in traits resulting from a common ancestor.
• Traits can have different functions but share similar underlying structures.
• Used for inferring evolutionary relationships.
• Studies the evolution of traits over time.

Homology Assessment

• Homology requires common origin at three levels:
  • Organism level: ontogeny (developmental stages).
  • Population level: tokogeny (within sexually reproducing species), studying features such as phenotype, chromosome number, and phylogeography.
  • Species level: phylogeny (across taxa or groups). Analyzing homology requires character compatibility, parsimony, and Bayesian likelihood analysis.
• Homology through:
  • Organogenetic studies
  • Same cell lineage: organs
  • Same tissue position: tissue
  • Same precursor molecule: molecules
  • Same initial sequence: genes

Divergent and Convergent Evolution

• Divergent: two or more species sharing a common ancestor, evolve and develop differing traits over time.
• Convergent: unrelated or distantly related species independently evolve similar features or traits in response to similar conditions (e.g., sharks and ichthyosaurs).

Taxa

• Collections of organisms.
• "Species" are terminal entities, but taxonomic units bigger than species are often arbitrarily defined, in the sense of monophyly.
• Operational Taxonomic Units (OTUs) and Hypothetical Taxonomic Units (HTUs).

Tree Interpretation

• Central objects of systematic analysis.
• Cladograms (Hennig) – nested sister-group relationships.
• Trees – series of ancestors-descendants statements.
• Scenarios – explanations in terms of evolution, ecology, or related biological or geological factors.

Cladogram, Tree, Scenario

• Diagrams illustrating evolutionary relationships.
• Showing ancestors/descendants.
• Examples of scenarios: drought, increased oxygen, egg, parasite.

Phylogenetic Trees

• Genealogical representations of a gene.
• Branch lengths reflect estimated evolutionary change (number of character changes).
• Nodes are points where taxa diverge/speciate.
• Outgroup is the basal taxon (farthest relative).
• Clade/cluster/group consists of organisms sharing a common ancestor.

Reading and Interpreting Trees

• Topology: the branching pattern of a tree; same topology means the same branching order and placement of groups.
• Branch lengths: represent the number of character changes between lineages.
• Nodes: branching points separating ancestral and descendant lineages.
• Root: the most ancestral lineage in a phylogenetic tree.

Confidence and Uncertainty in Phylogenetics

• Methods to assess uncertainty in phylogenies include bootstraps, maximum likelihood, and Bayesian approaches.

Phylogenetic Trees

• Details about monophyletic, paraphyletic, and polyphyletic groups are explained in terms of ancestry, common traits, and shared traits.
• Uses clades and/or clusters.

Assumptions about Trees

• Apomorphy: specialized or derived character state.
• Synapomorphy: derived character state shared by two or more groups.
• Autapomorphy: derived character state unique to one group.
• Symplesiomorphy: primitive or ancestral trait.

Explore the fundamental principles of systematics and phylogeny covered in BIO 110. This quiz tests your understanding of characters, homology, and the interpretation of phylogenetic trees. Deepen your knowledge of how organisms are classified and the relationships between different species.