Biological Classification, Phylogeny, and Cladistics

Principles of Classification and Binomial Nomenclature

• The Linnaean System and Classification: Biologists classify and name organisms using a systematic approach known as the Linnaean classification system. This system is inherently hierarchical.
• Binomial Nomenclature: This is the two-part scientific naming system for species.     * The Name Components: A species name consists of two parts: the genus and the specific epithet.         * Genus: The first word of the scientific name. This represents a group of closely related species. For example, the genus for humans is Homo.         * Specific Epithet: The second part of the name, which is unique for each member within a genus. It is often a descriptive term. For example, in Quercus alba (white oak), alba means "white." In Quercus rubra (red oak), rubra means "red."     * Naming Examples:         * Panthera pardus (Leopard).         * Homo sapiens (Humans). Note: The species name is Homo sapiens, not just sapiens.
• Rules for Writing Scientific Names:     * Capitalization: The first letter of the genus is always uppercase (capitalized), and this is the only letter in the scientific name that is capitalized.     * Formatting: The entire name (both words) must be italicized when typed. If handwritten, the name must be underlined (e.g., Quercus alba).     * Distinction from Common Names: We do not underline or follow strict capitalization rules for common names. Scientific names are utilized to avoid the ambiguity of common names.     * Abbreviation: Once a scientific name has been written out in full once in a paper or summary, the genus can be abbreviated to its first letter (e.g., P. pardus). The specific epithet is never abbreviated.

The Taxonomic Hierarchy

• Taxa (Taxon, singular): These are the formal units or categories of the hierarchy.
• The Hierarchical Levels: Biologists group species into increasingly inclusive categories. From the narrowest (most specific) to the broadest (most inclusive), they are:     1. Species: The most specific level (e.g., Panthera pardus).     2. Genus: A group of related species (e.g., Panthera).     3. Family: Genera grouped together (e.g., Felidae).     4. Order: Families grouped together (e.g., Carnivora).     5. Class: Orders grouped together (e.g., Mammalia).     6. Phylum: Classes grouped together (e.g., Chordata).     7. Kingdom: Phyla grouped together (e.g., Animalia).     8. Domain: The broadest category. All life is divided into three domains.
• The Three Domains of Life:     * Domain Bacteria: Prokaryotic organisms.     * Domain Archaea: Also prokaryotic, but distinct enough from bacteria to be in a separate group. They share some characteristics with Eukarya and some with Bacteria.     * Domain Eukarya: Organisms with a nucleus and organelles. This includes the kingdoms Animalia, Plantae, and Fungi, as well as various microorganisms like algae.

Phylogeny and Evolutionary Relationships

• Definition of Phylogeny: A phylogeny represents the evolutionary history and relationships between organisms. It is frequently reflected in the classification system but is not identical to it.
• Phylogenetic Trees as Hypotheses: A phylogenetic tree is a scientific hypothesis—an interpretation or "guess" of how organisms are related based on their characteristics.     * Support: Hypotheses may be supported or unsupported by new data.     * Debate: In evolutionary biology, major debates occur at scientific conferences regarding why certain taxa are placed in specific locations on a tree.
• Branch Points and Divergence: A branch point on a tree represents the divergence of two evolutionary lines from a common ancestor.
• Sister Taxa: Groups of organisms that share an immediate common ancestor not shared by any other group (e.g., humans and chimpanzees in certain phylogenies).
• Basal Taxon: A taxon that diverges very early in the history of a group and remains on a lineage that does not branch further. It originates near the most recent common ancestor of the entire group.
• Rooted Trees: A rooted phylogeny includes a branch representing the most recent common ancestor of all the taxa shown in that tree.
• Patterns of Descent vs. Phenotypic Similarity: Phylogenies show patterns of descent, not necessarily physical (phenotypic) similarities. Organisms may look different but be closely related evolutionarily, or look similar due to other factors.
• Limitations of Trees:     * They do not necessarily tell us when a species evolved or how much change occurred unless specifically scaled (and even then, it is often an estimate).     * One cannot assume a taxon evolved from the taxon next to it; they both evolved from a common ancestor.
• Rotation of Branch Points: Branch points can be rotated around the node without changing the evolutionary relationships being represented.

Cladistics and Grouping Organisms

• Cladistics: A method of grouping organisms by common ancestry. The goal is to define clades.
• Clade: A group of organisms consisting of an ancestral species and all its descendants. Clades are nested within larger clades.
• Types of Groupings:     1. Monophyletic: A valid clade consisting of the ancestor and all its descendants.     2. Paraphyletic: A grouping that includes an ancestral species and some, but not all, of its descendants. (Example: Leaving out cetaceans when looking at even-toed ungulates).     3. Polyphyletic: A grouping that includes distantly related species but does not include their most recent common ancestor.
• Reclassification: Biologists avoid polyphyletic and paraphyletic groupings. For instance, the Kingdom Protista was found to be highly polyphyletic; it was a "catch-all" for organisms that didn't fit elsewhere, but molecular data showed they were not all closely related.

Character States in Phylogeny

• Homologous Characters: Characters shared due to common ancestry, used to construct trees (anatomical, biochemical, or DNA sequence data).
• Shared Ancestral Character (Symplesiomorphy): A character that originated in an ancestor of the taxon. For example, all mammals have backbones, but the backbone does not distinguish mammals from other vertebrates because the ancestor of all vertebrates had a backbone.
• Shared Derived Character (Synapomorphy): An evolutionary novelty unique to a particular clade. For example, hair is a derived character for mammals; it is not found in their distant vertebrate ancestors.
• Character Context: Whether a character is ancestral or derived depends on the context of the phylogeny being studied. A backbone is a derived character if you go back far enough to the origin of vertebrates.
• Apomorphy: A general term for a derived character.
• Synapomorphy: An apomorphy shared by more than one group.

Inferring Phylogenies and Using Molecular Data

• In-group vs. Out-group: To build a tree, biologists compare the groups being studied (in-group) with a closely related comparison group (out-group) that diverged earlier. Any character found in both is considered ancestral.
• Character Tables: Tables use numbers to represent characters: $0$ for the absence of a character (ancestral/pleisiomorphic) and $1$ for the presence of a character (derived/apomorphic).
• Branch Lengths:     * In some trees, branch lengths are equal (standard).     * Proportional Lengths: Branch lengths can reflect the number of genetic changes in a DNA sequence.     * Timescale Lengths: Based on fossil evidence, branch lengths can provide a rough estimate of when specific divergence events occurred.

Maximum Parsimony

• The Principle of Parsimony: Biologists look for the "simplest explanation"—the tree that requires the fewest evolutionary changes or steps.
• Applying Parsimony:     * Morphological: The best tree is the one with the fewest appearances/disappearances of shared derived characters.     * Molecular (DNA): The best tree is the one with the fewest base-pair/nucleotide changes across the sequence.
• Step-by-Step DNA Parsimony Analysis:     1. Draw all possible tree hypotheses for the species (e.g., 3 species result in 3 possible trees).     2. Tabulate the DNA sequence at specific sites (Site 1, Site 2, Site 3, Site 4) for the ancestral out-group and the species in the in-group.     3. Count the number of changes required for each site on each potential tree.     4. Total the changes for each tree. The tree with the lowest total count (e.g., 6 changes vs. 7 changes) is the most parsimonious and thus the supported hypothesis.

Questions & Discussion

• Final Exam Logistics:     * Time: It is a 2-hour period starting at 9:00.     * Format: The exam will be the same length and format as previous exams, despite the longer time block provided.
• Student Question: If we have to solve a parsimony problem on the exam, will you provide the chart?
• Professor Response: Yes, a character table or chart is necessary to solve the problem. One cannot practically put together a phylogeny without the data (sites and characters) provided. The process could also be worked backward from a phylogeny to a character table.