Chapter 26: Phylogeny and the Tree of Life

Investigating the Tree of Life

Understanding the evolutionary relationships among organisms is a central theme in biology. The study of these relationships helps scientists classify life and trace the origins of species.

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

• Systematics: The scientific discipline that classifies organisms and determines their evolutionary relationships.

• Example: Phylogenetic analysis shows that legless lizards and snakes evolved from different lineages of legged lizards.

Binomial Nomenclature

To standardize the naming of species, biologists use a two-part scientific naming system developed by Carolus Linnaeus in the 18th century.

• Binomial: The two-part scientific name of a species.

• Genus: The first part of the name; always capitalized and italicized.

• Specific epithet: The second part; unique for each species within the genus and italicized.

• Example: Panthera pardus (leopard) — Panthera is the genus, pardus is the specific epithet.

Hierarchical Classification

Linnaeus introduced a hierarchical system for grouping species into increasingly inclusive categories.

• Taxonomic ranks (from broadest to most specific): Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

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

• Note: Broader taxa are not always directly comparable between lineages.

Example of Hierarchical Classification

Classification and Phylogeny

Classification and phylogeny are related but not always identical. Modern systematists prefer classification systems that reflect evolutionary relationships.

• Phylogenetic tree: A diagram representing evolutionary relationships among organisms.

• Branch point: Represents the divergence of two evolutionary lineages from a common ancestor.

• Sister taxa: Groups that share an immediate common ancestor.

• Rooted tree: Includes a branch representing the most recent common ancestor of all taxa in the tree.

Interpreting Phylogenetic Trees

Phylogenetic trees are hypotheses about evolutionary relationships. They show patterns of descent, not phenotypic similarity, and do not indicate the timing or amount of evolutionary change.

• Branches can be rotated without changing relationships.

• Phylogenetic trees can be drawn in various orientations (vertical, horizontal, diagonal).

• Do not assume that taxa next to each other evolved from one another.

Inferring Phylogenies: Morphological and Molecular Data

Systematists use morphological, genetic, and biochemical data to infer phylogenies.

• Homology: Similarity due to shared ancestry (e.g., similar bone structures).

• Analogy: Similarity due to convergent evolution, not shared ancestry (e.g., wings of birds and insects).

• Convergent evolution: Independent evolution of similar features in different lineages due to similar environmental pressures.

• Homology is distinguished from analogy by comparing fossil evidence and complexity of structures.

Cladistics and Clades

Cladistics groups organisms by common ancestry. A clade includes an ancestral species 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 most recent common ancestor.

Comparison of Group Types

Shared Ancestral and Derived Characters

Characters are used to infer evolutionary relationships.

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

• Shared derived character: Evolutionary novelty unique to a particular clade.

• Outgroup comparison helps distinguish ancestral from derived characters.

Phylogenetic Trees with Proportional Branch Lengths

Some trees use branch length to represent the number of genetic changes or time elapsed.

• Branch length can reflect genetic change or time since divergence.

• Fossil record can help calibrate branching points.

Maximum Parsimony and Maximum Likelihood

Systematists use principles to select the best phylogenetic tree from many possibilities.

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

• Maximum likelihood: The tree most likely to have produced the observed data, based on probability rules about DNA changes.

• Computer programs assist in finding the most parsimonious and likely trees.

Genome Evolution: Orthologous and Paralogous Genes

Comparing genes across species helps trace evolutionary history.

• Orthologous genes: Found in a single copy in the genome and homologous between species; diverge after speciation.

• Paralogous genes: Result from gene duplication; found in more than one copy in the genome and can evolve new functions within a species.

• Gene duplication increases opportunities for evolutionary change and leads to gene families.

• Complexity of an organism is not strictly linked to the number of genes.

Molecular Clocks

Molecular clocks estimate evolutionary time by assuming a constant rate of molecular change.

• Useful for extending phylogenies beyond the fossil record.

• Genes that evolve at different rates are used to investigate events at different timescales (e.g., rRNA for ancient divergences, mtDNA for recent events).

Additional info: These notes expand on brief slide points and fragmented text to provide a coherent, self-contained study guide suitable for college-level General Biology students.