Phylogeny and the Tree of Life (Chapter 26): Classification, Cladistics, and Molecular Evolution

Phylogeny and the Tree of Life

Introduction to Biological Classification

Biological classification organizes living organisms into hierarchical groups based on shared characteristics and evolutionary relationships. This system helps scientists communicate about species and understand the diversity of life.

• Taxonomy: The science of naming, describing, and classifying organisms.

• Systematics: The study of the diversity of organisms and their evolutionary relationships.

• Phylogeny: The evolutionary history of a species or group of related species.

Linnaean Classification System

Hierarchical Taxonomic Ranks

The Linnaean system classifies organisms into a series of ranked categories, from broadest to most specific. Each level is called a taxon (plural: taxa).

• Domain: The highest taxonomic rank; three domains are Bacteria, Archaea, and Eukarya.

• Kingdom: Groups within each domain (e.g., Animalia in Eukarya).

• Phylum: Groups of related classes (e.g., Chordata).

• Class: Groups of related orders (e.g., Mammalia).

• Order: Groups of related families (e.g., Carnivora).

• Family: Groups of related genera (e.g., Felidae).

• Genus: Groups of related species (e.g., Panthera).

• Species: The most specific level; a group of individuals that can interbreed (e.g., Panthera pardus, the leopard).

Example: The classification of the leopard (Panthera pardus):

Rank	Example
Domain	Eukarya
Kingdom	Animalia
Phylum	Chordata
Class	Mammalia
Order	Carnivora
Family	Felidae
Genus	Panthera
Species	Panthera pardus

Phylogenetic Trees and Cladistics

Understanding Phylogenetic Trees

Phylogenetic trees are branching diagrams that depict evolutionary relationships among species or groups. They are constructed using morphological and genetic data.

• Branch: Represents a lineage.

• Node: Represents a common ancestor.

• Clade: A group consisting of an ancestor and all its descendants (monophyletic group).

Phylogenetic trees can be drawn in various styles (vertical, diagonal) but convey the same relationships.

Types of Groups in Cladistics

• Monophyletic group (clade): Includes an ancestor and all its descendants.

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

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

Group Type	Definition
Monophyletic	Ancestor + all descendants
Paraphyletic	Ancestor + some descendants
Polyphyletic	Distantly related species, not including common ancestor

Homology and Analogy

Comparing Traits

• Homologous traits: Similarities due to shared ancestry (e.g., forelimb bones in mammals).

• Analogous traits: Similarities due to convergent evolution, not common ancestry (e.g., wings of bats and insects).

Example: The bones in a human arm, cat leg, whale flipper, and bat wing are homologous structures, indicating common ancestry.

Cladistics: Building Phylogenies

Principles of Cladistics

Cladistics is a method of classifying organisms based on common ancestry. It uses shared derived characters (synapomorphies) to group taxa.

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

• Shared derived character: Unique to a particular clade.

• Outgroup: A species or group closely related to, but not part of, the group being studied (ingroup).

Constructing Cladograms

• Cladograms are diagrams showing the branching patterns of evolution.

• Groups are nested within larger clades based on shared derived characters.

Methods for Building Phylogenetic Trees

Maximum Parsimony

This method assumes that the simplest explanation (fewest evolutionary changes) is most likely correct.

• For DNA data, the tree with the fewest base changes is preferred.

Maximum Likelihood

This method identifies the tree most likely to have produced the observed DNA data, based on specific models of genetic change.

• Uses probability rules about how DNA changes over time.

Gene Duplications and Gene Families

Types of Homologous Genes

• Orthologous genes: Homology is the result of a speciation event; genes found in different species.

• Paralogous genes: Homology results from gene duplication; genes found within the same species.

Example: Cytochrome c genes in humans and dogs are orthologous; olfactory receptor genes in humans are paralogous.

Genome Evolution

Patterns in Genome Evolution

• Gene duplication increases genetic material, allowing for evolutionary innovation.

• Lineages that diverged long ago often share many orthologous genes (e.g., humans and mice share 99% of their genes as orthologs).

• Gene number does not always correlate with organismal complexity.

Example: Humans have only about four times as many genes as yeast, but human genes are more versatile.

Molecular Clocks

Estimating Evolutionary Time

Molecular clocks use the rate of genetic mutations to estimate the time since two species diverged from a common ancestor.

• Assumes some genes evolve at a relatively constant rate.

• Calibrated using fossil record data and known divergence times.

• Number of nucleotide substitutions is proportional to time since divergence for orthologous genes, or since duplication for paralogous genes.

Limitations of Molecular Clocks

• Some genes evolve at irregular rates.

• Rates can vary between lineages and genes.

• Not all evolutionary events are clocklike.

Modern Classification: The Three-Domain System

Current Understanding of Biological Diversity

• Three domains: Bacteria, Archaea, and Eukarya.

• Within Eukarya: Kingdoms include Protista, Fungi, Plantae, and Animalia.

Domain	Kingdoms
Bacteria	Eubacteria
Archaea	Archaebacteria
Eukarya	Protista, Fungi, Plantae, Animalia

Additional info: Some context and terminology were inferred and expanded for clarity and completeness, based on standard General Biology curriculum.