Chapter 26

Chapter 26: PHYLOGENIES AND CLASSIFICATION

Key Concepts

• Phylogenies

  • Show evolutionary relationships.

  • Inferred from morphological and molecular data.

  • Shared characters are used to construct phylogenetic trees.

  • An organism’s evolutionary history is documented in its genome.

  • Molecular clocks help track evolutionary time.

  • Understanding of the tree of life continues to change based on new data.

Investigating the Tree of Life

• Dinosaurs are more closely related to birds than to crocodiles.

• Dinosaurs, birds, and crocodiles are all classified as Archosaurs.

Evidence Linking Birds to Dinosaurs

• Discovery of feather dinosaur fossils provides evidence of the link.

Phylogeny

• Defined as the evolutionary history of a species or group of related species.

• Example: Lizards, snakes, crocodilians, and their common ancestor.

Systematics

• Classifies organisms and determines their evolutionary relationships.

• Utilizes:

  • Fossils

  • Molecular data

  • Genetic data

Taxonomy

• Discipline concerned with classifying and naming organisms.

Binomial Nomenclature

• Developed by Carolus Linnaeus in the 18th century.

• Two key features:

  1. Two-part names for species.

  2. Hierarchical classification.

• Example: Species name format is italicized, e.g., Homo sapiens.

Hierarchical Classification

• Groups species into broader categories:

  • Domain

  • Kingdom

  • Phylum

  • Class

  • Order

  • Family

  • Genus

  • Species

• Taxon: A taxonomic unit at any level of hierarchy.

Linking Classification and Phylogeny

• Systematists depict evolutionary relationships in branching phylogenetic trees.

• A phylogenetic tree represents a hypothesis about evolutionary relationships.

• Each branch point denotes the divergence of two species.

• Sister taxa: Groups sharing an immediate common ancestor.

Types of Phylogenetic Trees

• Rooted tree: Includes a branch to represent the last common ancestor.

• Basal taxon: Diverges early in the history of a group.

• Polytomy: A branch from which more than two groups emerge.

Insights from Phylogenetic Trees

• Show patterns of descent, not phenotypic similarity.

• Do not indicate the timing of species evolution or the extent of change.

Morphological and Molecular Data

• Systematists gather information on:

  • Morphologies

  • Genes

  • Biochemistry of organisms.

Analyzing Homologies

• Homologies: Similarities due to shared ancestry.

• Analogies: Similarities due to convergent evolution.

Convergent Evolution

• Occurs when environmental pressures produce similar adaptations in unrelated species.

Example of Homology vs. Analogy

• Bat and bird wings are homologous as forelimbs but analogous as wings.

• Homoplasies: Analogous structures that evolved independently.

Evaluating Molecular Homologies

• Systematists analyze DNA segments to identify homologies.

• Mathematical tools help distinguish homology from analogy in molecular data.

Cladistics

• Groups organisms by common descent.

• Clade: A group of species that includes an ancestral species and all its descendants.

• Clades can be nested but not all groupings qualify.

  • Monophyletic: Includes an ancestor and all descendants.

  • Paraphyletic: Includes an ancestor and some descendants.

  • Polyphyletic: Includes unrelated species without their common ancestor.

Shared and Derived Characters

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

• Shared derived character: Unique evolutionary novelty to a particular clade.

Inferring Phylogenies Using Characters

• Distinction between shared derived and ancestral characters is vital.

• An outgroup: Closely related group diverged before the ingroup.

Maximum Parsimony and Maximum Likelihood

• Principles to narrow possibilities of phylogenetic trees:

  • Maximum parsimony: Tree with fewest evolutionary events is most likely.

  • Maximum likelihood: Finds tree reflecting the most likely sequence of events.

Phylogenetic Trees as Hypotheses

• Fit the most data - morphological, molecular, biochemical, and fossil evidence.

Interpreting Cladograms and Phylogenetic Trees

• Cladograms: Depict only branch order.

• Phylograms: Branch lengths indicate evolutionary change.

  • Can represent chronological time.

Applying Phylogenies

• Phylogeny provides insights about characteristics in related species.

• DNA can trace illegal hunting origins through phylogenetic analysis.

Molecular Markers in Species Identification

• Use of cytochrome oxidase (CO1) gene sequence as a DNA barcode for identifying species.

Evolutionary History in Genomes

• Comparing molecules for relatedness helps trace evolutionary history.

• rRNA changes slowly; useful for ancient branching points.

• mtDNA evolves rapidly; used for recent evolutionary events.

Gene Duplications and Gene Families

• Increase gene numbers and evolutionary opportunities.

• Duplicated genes can diverge and evolve new functions.

Genome Evolution

• Variety of species share orthologous genes indicating shared ancestry.

• Gene number does not correlate with complexity.

Molecular Clocks

• Used to estimate evolutionary time based on constant rates of evolution.

• Adjusted with known branch dates from fossil records.

Problems with Molecular Clocks

• Irregularities arise from natural selection favoring certain DNA changes.

• Older divergence estimates are more uncertain.

Applying Molecular Clocks

• Example: Analysis of HIV strains tracking its evolution and spread.

Changing Understanding of Phylogenetic Relationships

• New data from molecular systematics reshapes the tree of life.

Transition from Kingdoms to Domains

• Initial two-kingdom system expanded to five kingdoms, then to three domains (Bacteria, Archaea, Eukarya).

Horizontal Gene Transfer

• Genes exchange significantly between organisms, impacting evolution.

• Represents a tangled web rather than a simple tree.

Final Perspective

• The early history of life depicted as interconnected branches due to horizontal gene transfer.