Taxonomy

Identifying, naming, and classifying species into a hierarchical structure based on shared traits and genetic relationships.

• This helps see the similarities between species from the past evolution and changes throughout time.
• Structural, evolutionary and functional similarities

Example: Humans

Domain	Eukarya
Kingdom	Animalia
Phylum	Chordata
Class	Mammalia
Order	Primates
Family	Hominidae
Genus	Homo
Species	Homo sapiens

Binomial Nomenclature

Each species has a two part latin name: Genus Species

• Genus is capitalized, while the species is lowercase
• It should be italicized or underlined

Domains

Bacteria (Prokaryotic)

• Found almost everywhere (soil, water, inside organisms)
• Unique bacterial genes
• Sensitive to antibiotics
• Cell wall made of peptidoglycan
• Circular DNA, no nucleus
• Small ribosomes (70S)
• Uses binary fission for reproduction
• Some produce endospores (for surviving harsh conditions)
• No introns in most genes

Archaea (Prokaryotic, but genetically different)

• Often in extreme environments (hot, salty, acidic) but also found in normal places
• Cell wall does not have peptidoglycan
• Membrane lipids use ether bonds (more stable in heat)
• Genes and enzymes are more similar to eukaryotes
• Resistant to antibiotics
• Ribosomes structurally closer to eukaryotic (70S but more complex)
• Uses binary fission
• Can produce methane (e.g., methanogens)
• Has introns in some genes
• Start codon codes for methionine (like eukaryotes)

Eukarya (animals, plants, fungi, protists)

• Has nucleus and membrane-bound organelles
• DNA is linear and stored in chromosomes
• Ribosomes are larger (80S)
• Can be unicellular or multicellular
• Can reproduce sexually (meiosis) or asexually (mitosis)
• Has introns in most genes
• Complex internal structure (e.g., ER, mitochondria, cytoskeleton)
• Some have cell walls (plants = cellulose, fungi = chitin)
• Not sensitive to antibiotics

Prokaryotes (Bacteria & Archaea) have no nucleus, single-celled, and use binary fission.
Eukaryotes have nucleus, more complex, larger cells. Archaea are more like eukaryotes in genetics and enzymes, but look like bacteria. Antibiotics only affect bacteria, not archaea or eukaryotes. Only eukaryotes can do mitosis and meiosis

Kingdom

Kingdom is a broad category used to organize living organisms by their major body plans, nutrition, and cell types.

• The big groups of life

Example (For Eukaryotic):

Kingdom	What's it includes	Features
Animalia	Animals (e.g., insects, mammals, birds, humans)	Multicellular, heterotrophic, no cell walls, move actively
Plantae	Plants (e.g., trees, mosses, grasses)	Multicellular, autotrophic (photosynthesis), cell walls with cellulose
Fungi	Mushrooms, molds, yeasts	Heterotrophic, cell walls with chitin, absorb nutrients

Phylum

A phylum is the level of classification below Kingdom and above Class. It groups organisms based on major structural features and body plans that come from a common evolutionary ancestor.

In the Tree of Life, a phylum represents a major branch — meaning all members of a phylum share key traits that evolved from a single, ancient ancestor.

Phylum	Key Traits	Examples
Arthropoda	Segmented body, exoskeleton, jointed limbs	Insects, spiders, crustaceans
Chordata	Notochord (flexible rod), dorsal nerve cord	Mammals, birds, fish, reptiles
Mollusca	Soft body, many with shells, muscular foot	Snails, octopuses, clams
Annelida	Segmented, tube-like bodies, bristles	Earthworms, leeches

Class

A class groups together related orders. Organisms in the same class share general body plans, functions, and evolutionary traits.

In biological classification, a class is a taxonomic rank that groups together organisms within the same phylum that share important structural and functional traits. It describes a broad set of organisms that have similar body plans, developmental patterns, and evolutionary history.

• "What general kind of organism is this?"

Class	Examples
Mammalia	Mammals (Humans, Whales, Dogs)
Aves	Birds
Reptilia	Reptiles (Snakes and Lizards)

Order

In biological classification, an order is a taxonomic rank below class and above family. It groups together organisms that belong to the same class and share even more specific structural, functional, or evolutionary traits.

Order	Examples
Carnivora	Dogs, cats, bears
Cetacea	Whales, dolphins
Lepidoptera	Butterflies, moths

Family

In biological classification, a family is a taxonomic rank below order and above genus. It groups together organisms within the same order that are even more closely related and share very specific structural, genetic, or evolutionary traits.

Example:

The Hominidae family (called the "great apes") includes:

• Humans (Homo sapiens)
• Chimpanzees (Pan troglodytes)
• Gorillas (Gorilla gorilla)
• Orangutans (Pongo pygmaeus)

These organisms share:

• Large brains
• No tails
• Complex social behavior
• Similar DNA

Genus

In biological classification, a genus is the taxonomic rank below family and above species. It groups together very closely related species that are structurally similar and share a recent common ancestor.

A genus is like the last name of a group of closely related organisms. Members of the same genus are more alike than those just in the same family, but they are still different species.

Example:

The genus Homo includes:

• Homo sapiens (modern humans)
• Homo neanderthalensis (Neanderthals)
• Homo habilis (an early human ancestor)

They all share:

• Upright posture
• Tool use
• Larger brains compared to other primates

Species

A species is the most specific rank in the taxonomic hierarchy. It refers to a group of organisms that:

• Can interbreed in nature
• Produce fertile offspring
• Share the same physical and genetic characteristics.

A species is a group of organisms that are so similar they can mate and have babies that can also reproduce.

Phylogenetic Tree

Phylogenetics is the study of the evolutionary relationships among organisms. Scientists use DNA, proteins, and physical traits to figure out how species are connected through common ancestors. The result is often shown in a phylogenetic tree: a branching diagram that represents these relationships.

A phylogenetic tree is a scientific diagram that shows how closely different species are related based on their evolutionary history.

It tells us:

• Which species share a common ancestor
• How long ago they split (diverged) from each other
• Which species are more closely related

Structure:

• Branches = species or groups
• Nodes (branching points) = a common ancestor
• Closer branches = more closely related

Example:

• Common Ancestor
  • Adalia bipunctata (Two-spotted Lady Beetle)
  • Coccinella septempunctata (Seven-spotted Lady Beetle)
  • Propylsa japonica
  • Harmonia axyridis (Asian Lady Beetle)
• Hippodamia convergens
  • Coleomegilla maculata
• Chilocorus stigma (Twice-stabbed Lady Beetle)

Cladistics

Cladistics is a method used in phylogenetics to group organisms into clades. A clade includes an ancestor and all of its descendants—like a branch on the tree of life.

Cladistics focuses on shared derived traits (new traits that evolved in the most recent common ancestor).

It's about classifying organisms based on evolutionary history, not just appearance.

Cladogram	Phylogenetic Tree
Order of evolutionary branching	Evolutionary relationships and time/distance
Visualizes shared traits and clades (common ancestors + descendants)	Traces real evolutionary history using DNA, morphology, etc.
Branch length doesn't mean anything	Branches are scaled to data
Trait-based grouping (cladistics)	Evidence-based evolutionary patterns (phylogenetics)

Sources

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