Scientific Naming and Classification

Scientific Nomenclature and Phylogeny

Biologists use scientific naming and classification to organize and understand the diversity of life. This process involves assigning unique names to species and grouping them based on evolutionary relationships.

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

• Systematics: The discipline focused on classifying organisms and determining their evolutionary relationships.

• Linnaean System: Each species is given a unique name consisting of two parts: Genus and Species epithet.

Original Kingdoms

• Monera – prokaryotes

• Protista – single cell eukaryotes, algae

• Fungi – mushrooms, fungus

• Plantae – plants

• Animalia – animals

Modern Classification

• Three domains: Archaea, Bacteria, Eukarya

Rules for Naming

• Names must be Latin or derived from Latin

• Best names are informative (e.g., Octopus = 8 legs)

Phylogenetic Trees and Systematics

Building Phylogenetic Trees

Phylogenetic trees represent evolutionary relationships among organisms. They are constructed using shared characteristics and genetic data.

• Pick a group with at least one shared characteristic

• Find distinguishing features

• Choose an outgroup for comparison

• Use rules: scoreable traits, homologous characteristics, and computer analysis

• Principle of Parsimony: The simplest explanation is most likely correct

Types of Groups

• Monophyletic: Group with ancestor and all descendants (best)

• Paraphyletic: Group with ancestor and some, but not all, descendants

• Polyphyletic: Group with unrelated organisms

Phylogenetic Bracketing

• Used to predict features in extinct organisms (e.g., dinosaurs)

• Shared features among birds and crocodiles suggest dinosaurs had those features

Origin of Life and Fossils

Steps Leading to Life on Earth

The origin of life on Earth involved several key steps, beginning about 4.6 billion years ago.

• Formation of Organic Molecules: Simple molecules formed in early atmosphere and oceans

• Formation of Macromolecules: Organic molecules assembled into polymers

• Formation of Protocells: Macromolecules packaged into cell-like structures

• RNA for Replication: "RNA first" hypothesis; RNA can self-replicate and act as an enzyme

Fossils and Dating Methods

• Fossils found in sedimentary rock strata

• Trace fossils: footprints, burrows, etc.

• Relative dating: age determined by position in rock layers

• Radiometric dating: uses isotopes with known half-lives

Prokaryotes: Structure and Diversity

Characteristics of Prokaryotes

Prokaryotes are single-celled organisms classified into Bacteria and Archaea. They are among the most abundant and diverse life forms on Earth.

• Most are unicellular; some form colonies

• Shapes: cocci (spheres), bacilli (rods), spirilla (spirals)

• Gram Staining: distinguishes between Gram-positive and Gram-negative bacteria

Gram Staining

• Gram-positive: Thick peptidoglycan layer, easier to treat with antibiotics

• Gram-negative: Thin peptidoglycan, outer membrane with lipopolysaccharides, harder to treat

Endospores

• Some bacteria form endospores to survive harsh conditions

• Endospores can remain viable for centuries

Symbiosis

Types of Symbiotic Relationships

Symbiosis refers to two different species living closely together, often with significant effects on each other.

Genetic Diversity in Prokaryotes

Mechanisms of Genetic Exchange

Prokaryotes increase genetic diversity through several mechanisms, even though they reproduce asexually by binary fission.

• Conjugation: DNA transferred between two prokaryotic cells via direct contact

• Transformation: Uptake of foreign DNA from surroundings

• Transduction: Transfer of DNA by bacteriophages (viruses)

Prokaryotes in the Environment and Human Health

Roles and Impacts

Prokaryotes play essential roles in nutrient cycling, decomposition, and human health. Some are beneficial, while others cause disease.

• Decomposers recycle nutrients

• Symbiotic relationships with humans (e.g., gut bacteria)

• Pathogenic bacteria cause diseases (e.g., tuberculosis, Lyme disease)

• Antibiotic resistance is a growing concern

Antibiotic Resistance

• Resistance has evolved due to overuse and misuse of antibiotics

• New antibiotics and treatments are continually being developed

Major Events in Evolution

Origin of Prokaryotes and Eukaryotes

Earth formed about 4.6 billion years ago. The first prokaryotes appeared 3.5–3.8 billion years ago, followed by the evolution of eukaryotes about 2 billion years ago.

• Oxygen Revolution: Cyanobacteria produced oxygen via photosynthesis, changing Earth's atmosphere

• Endosymbiosis: Eukaryotic cells acquired mitochondria and chloroplasts by engulfing prokaryotes

Relationship to Oxygen

• Aerobes: Require oxygen

• Anaerobes: Die with oxygen

• Facultative Anaerobes: Can live with or without oxygen

Locomotion, Nutrition, and Ecosystem Roles

Characteristics of Eukaryotes

Eukaryotes exhibit diverse forms of locomotion and nutrition, contributing to their ecological roles.

• Locomotion: Sessile (do not move), cilia, flagella, pseudopodia

• Nutrition: Autotrophs (photosynthesis), heterotrophs, decomposers, symbionts

• First eukaryotes: Appeared 1.6–2.1 billion years ago; ancestors of multicellular life

Origin of Multicellularity

Steps to Multicellularity

Multicellularity evolved multiple times, allowing organisms to become more complex and specialized.

• Colony formation: cells stick together after division

• Increase in cell communication and adhesion

• Cell specialization: different cells perform specific functions

Why Multicellularity?

• Predation avoidance

• Improved access to nutrients

• Cell specialization for complex tasks

Major Multicellular Groups

• Fungi

• Plantae

• Animalia

Evolutionary Developmental Biology

Heterochrony and Homeotic Genes

Changes in developmental timing and gene regulation can drive evolutionary change in body plans and structures.

• Heterochrony: Change in rate or timing of developmental events

• Homeotic genes: Master regulatory genes that determine body plan organization

• Hox genes: Provide positional information in embryos

Additional info: This guide expands on brief notes with definitions, examples, and context for key biological concepts.