Diversity Among Organisms: Taxonomy and Phylogenetics

Introduction to Diversity

• This unit transitions from meiosis, genetics, evolution, and population genetics into the study of diversity among organisms.

• Today's focus is on how diversity is studied, described, and visually depicted.

• Future topics will include plants (leading up to fall break), animals (after fall break), and eventually community and ecosystem dynamics.

• Notes will encompass definitions, new vocabulary (often with sensible roots, grouped for easier learning), and new biological features, all organized around a central life cycle framework.

Taxonomy and Phylogenetics

• We are moving into two key biological disciplines: Taxonomy and Phylogenetics.

• Both fields are fundamentally interested in species relationships.

• The scope shifts from individual interactions within a population (microevolution) to the species as a whole, and then to the evolutionary relationships between different species.

Taxonomy: Naming and Grouping Organisms

• Definition: Taxonomy is the discipline (a system) of naming and grouping organisms, classifying them into categories.

• Historical Basis: Much of modern taxonomy is rooted in the work of Carolus Linnaeus, an 18th-century botanist.

  • Linnaeus observed similarities and differences among plants and developed an organizing system that applies to all types of organisms.

• Two Key Features of Linnaeus's System:

  1. Binomial Nomenclature

  2. Hierarchical Classification

Binomial Nomenclature

• Definition: A system of naming where every species receives a two-part name (''bi'' = two, ''nomenclature'' = naming system).

• Components of the Name:

  • First part: The genus name. This represents a broader category.

    • Plural: ''genera'' (not ''genuses'').

  • Second part: The species name, also called the specific epithet. This part acts like an adjective, describing the individual within its genus.

• Importance: Both parts are essential to uniquely designate a species.

  • Metaphor: Like a person's first and last name (e.g., Rebecca Penny). "Penny" is the genus (family group), "Rebecca" is the specific epithet (identifying individual within that group).

• Formatting Conventions:

  • The genus name is always capitalized.

  • The species epithet is always lowercase.

  • The entire two-part name is italicized.

    • Reason: Names are in Latin, and by convention, text written in a different language from the main one is italicized.

  • If handwriting, the name should be underlined instead of italicized.

• Examples:

  • Homo sapiens:

    • Genus: Homo

    • Specific epithet: sapiens (referring to higher consciousness, distinguishing our type of Homo).

  • Phyllictrum macrostylem:

    • Genus: Phyllictrum

    • Specific epithet: macrostylem (''macro'' = big, ''stylem'' = part of the flower, indicating the Phyllictrum with a big style).

Hierarchical Classification

• Concept: Organisms are grouped into a series of nested categories, moving from very broad and inclusive groups to progressively narrower and more exclusive ones.

• Terminology: A taxon (plural: taxa) refers to any category in this hierarchy (e.g., species is a taxon, genus is a taxon, family is a taxon).

• Linnaean Ranks (from most inclusive to most exclusive):

  • Domain (newest addition, above Kingdom: Eukaryotes, Prokaryotes - Bacteria, Archaea)

  • Kingdom

  • Phylum (or Division for plants)

  • Class

  • Order

  • Family

  • Genus

  • Species

• Mnemonic Device: A common one is "King Philip Came Over For Good Spaghetti" to remember the order of Kingdom, Phylum, Class, Order, Family, Genus, Species.

• Illustration (Plant Example):

  • Kingdom Plantae (very diverse, includes mosses, eggplants, maples, peas).

  • Division Magnoliophyta (flowering plants).

  • Class Magnoliopsida (a subset of flowering plants, excluding corn and grass).

  • Further down to Order, Family, Genus, and finally a single species (e.g., the mighty potato), each level becoming more specific.

Phylogenetics: Depicting Evolutionary Relationships

• Definition: Phylogenetics is a field that uses graphical representations (phylogenetic trees) to depict the evolutionary relationships among species, families, or any other taxa.

• Core Question: Which species share a common ancestor, and how recent was that common ancestor compared to others?

• Terminology:

  • Lineage: A sequence of ancestor and descendant populations over time. This concept applies to macroevolutionary changes (changes in overall characteristics, new forms/functions), rather than just microevolutionary changes in allele frequencies.

Components of a Phylogenetic Tree

• Tips/Ends of Branches: Represent the individual taxa (e.g., species A, B, C) that exist in the present day or are being studied.

• Branches: Represent evolutionary lineages, showing the historical path of descent.

• Nodes (Junctions or Internal Branch Points): Represent hypothetical common ancestors where lineages diverged.

  • A node is a hypothesis about a population that existed in the past; it's not necessarily a known fossil.

  • The ancestral population at a node may have looked like the descendant taxa, a mixture, or something quite different.

  • Nodes can also be conceptualized as barriers to gene flow (e.g., a mountain range, an island) that led to population splits.

• Time: Flows from left to right on the tree.

  • The leftmost points represent the most distant past.

  • The rightmost points (the tips) represent the most recent present.

Reading and Interpreting Phylogenies

• Sister Taxa: Two taxa that share a more recent common ancestor with each other than with any other group on the tree.

  • Example: If Taxon B and Taxon C share a common ancestor that is unique to them, B and C are sister taxa.

• Relatedness: The primary information conveyed by a phylogeny is relatedness, specifically the recency of shared common ancestry.

  • B and C are more closely related to each other than either is to A if they share a more recent common ancestor with each other.

• Similarity vs. Relatedness: A phylogeny does not directly indicate the degree of physical or genetic similarity, nor the amount of change that occurred along a branch.

  • Species that share a more recent common ancestor may be more similar and share more traits, but this is not always strictly true due to differential evolution (e.g., rapid change in one lineage, stasis in another).

  • When considering DNA sequences, more independent evolution time generally correlates with more accumulated genetic differences.

• Evolutionary Processes: Once lineages split, mutation, selection, genetic drift, etc., act independently on each separate lineage, leading to genetic and phenotypic divergence.

• Reading Direction: We typically read a phylogeny from right to left (from recent to past) to understand the evolutionary history.

• Tree Shape: The specific 'elbow' or 'triangle' shape of branches at nodes (whether rectangular or diagonal) carries no additional information; it's a visual choice.

Concept Check: Humans and Chimpanzees

• Question: Did humans descend from chimpanzees?

• Answer: No. Humans and chimpanzees share a common ancestor, but that ancestor was neither a chimpanzee nor a human. Both humans and chimpanzees represent distinct lineages that evolved from this shared ancestor, experiencing their own unique evolutionary changes.

Hierarchical Classification in a Phylogenetic Context

• Phylogenetic trees visually map species relationships and also illustrate the concept of hierarchical organization.

• Car-pooling Metaphor: Imagine a car trip where individuals represent lineages. While in the car, everyone shares information (common traits/evolutionary history). When someone gets out (a lineage diverges), they no longer share the ongoing conversation, though they retain traits acquired while in the car. They then develop their own separate experiences and traits. The earlier a lineage leaves, the fewer shared traits it has with the remaining lineages.

• Data for Building Phylogenies: Phylogenetic trees can be constructed using various types of data:

  • DNA sequences (genetic information)

  • Physical traits (morphology, e.g., presence of limbs, hair)

  • Behavioral traits

  • Physiological traits

• The tips of a phylogeny can represent species, populations, or even genes.

Ancestral vs. Derived Characters

• Character: A feature or trait, whether phenotypic or genetic, used in phylogenetic analysis.

• Ancestral Character: A character that was present in the common ancestor of the taxa being considered.

  • Example: If we consider turtles and leopards, the amniotic egg is an ancestral character because it was present in their common ancestor and is shared by both.

• Derived Character: A character that is novel (new) and unique to a particular group, relative to its ancestor.

  • Example: If an ancestor was quadrupedal, but a descendant lineage (e.g., Taxon B) evolved two-legged walking, two-legged walking would be a derived character for Taxon B.

• Context-Dependent: A character can be both ancestral and derived, depending on the specific group of taxa being analyzed.

  • Continuing the amniotic egg example: While ancestral for turtles and leopards together, if we consider a broader group including salamanders (which lack amniotic eggs), the amniotic egg would be a derived character for the