Phylogeny and the Tree of Life

Phylogeny and the Tree of Life

• Phylogeny refers to the evolutionary history of a species.
• Phylogenetic trees depict the evolutionary relationships between species using common ancestor, evolutionary lineage, sister taxa, nodes, and branches.
• Systematics involves studying the diversity of life and the relationships between organisms.
• Taxonomy classifies organisms into hierarchical categories like Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.
• Binomial Nomenclature names species by their genus and species, for example, Homo sapiens.
• Taxon refers to a group at any level of the taxonomic hierarchy.
• Cladistics classifies organisms based on shared derived characteristics (synapomorphies) from a common ancestor.
• A Clade is a group of organisms consisting of a common ancestor and all its descendants.
• Clades are considered monophyletic.
• An Outgroup is a species used as a reference to determine the evolutionary traits of the ingroup.
• Homologous traits arise from shared ancestry, versus analogous traits that arise due to convergent evolution.
• Molecular Clock is a method for estimating evolutionary divergence time using genetic mutations accumulating at a relatively constant rate.
• Maximum likelihood and maximum parsimony are techniques used to determine the most accurate phylogenetic trees.
• The broadest classification level is Domains, comprising Bacteria, Archaea, and Eukarya.
• Key vocabulary includes Shared ancestral, Shared derived character, Common Ancestor, Basal taxon, and Rooted tree.
• Synapomorphy is a shared, derived characteristic that defines a clade.
• Plesiomorphy is a shared, ancestral trait.
• Monophyletic refers to a group of organisms that includes a common ancestor and all its descendants.
• Paraphyletic refers to a group that includes a common ancestor but not all of its descendants.
• Polyphyletic refers to a group that includes organisms from different evolutionary backgrounds without a common ancestor.
• Hierarchical Classification contains major taxa (Domain, Kingdom, Phylum, etc.) and an example organism at all levels of classification.
• Phylogenetic trees show relationships based on common ancestry, not a progression of increasing complexity.

Prokaryotes

• Prokaryotes are unicellular organisms lacking a nucleus and membrane-bound organelles, classified into Bacteria and Archaea.
• Prokaryotic cells have a simple structure, including a Nucleoid (where DNA is located), Ribosomes, Plasmid, Capsule, and Plasma Membrane.
• The Plasma Membrane controls the movement of materials in and out of the cell.
• The Cell Wall provides structural support and protection, and in bacteria, often contains peptidoglycan.
• Flagella is used for locomotion.
• Fimbriae and Pili are hair-like structures involved in attachment and conjugation (genetic exchange).
• Gram Staining classifies bacteria into Gram-positive (thick peptidoglycan layer) and Gram-negative (thin peptidoglycan and outer membrane).
• Prokaryotes act as Pathogens, Mutualists, Symbionts, and are important for Chemical Recycling, Chemical Cycling (Nitrogen Fixation), and are used in food production.
• Prokaryotes reproduce asexually by binary fission, creating genetically identical offspring.
• Prokaryotes exchange genetic material through Transformation (uptake of foreign DNA), Conjugation (direct transfer of DNA), and Transduction (DNA transfer via bacteriophages).
• Prokaryotes have high genetic diversity and mutation rates.
• Prokaryotes are metabolically diverse and can be classified by how they obtain energy.
• Autotrophs synthesize their own food using sunlight (Photoautotroph) or inorganic compounds (Chemoautotroph).
• Heterotrophs obtain energy by consuming other organisms (Chemoheterotroph).
• Aerobes need oxygen, contrastingly Anaerobes do not.
• Facultative anaerobes can live with or without oxygen, versus obligate anaerobes which cannot live with oxygen.
• Bacteria is a domain that includes Cyanobacteria (photosynthetic), Proteobacteria (pathogens), and Firmicutes (pathogenic and beneficial bacteria).
• Archaea is a domain often found in extreme environments like hot springs and salt lakes.
• Common cell forms of prokaryotes include Spherical (cocci), Rod-shaped (bacillia), and spiral.
• Peptidoglycan is a polymer found in bacterial cell walls.
• Endospore is a dormant, resistant form of some bacteria that can survive extreme conditions.
• Plasmids are small, circular DNA molecules in bacteria that can carry extra genetic material, such as antibiotic resistance genes.
• Taxis refers to the ability to move toward or away from a stimulus (e.g. Chemotaxis, phototaxis).
• Extremophiles include halophiles, thermophiles, and methanogens.
• Most bacteria are harmless or beneficial.

Protists

• Protists are a diverse group of eukaryotic organisms that are mostly unicellular.
• Protists can be Protozoa (animal-like, heterotrophic, and motile), Algae (plant-like and photosynthetic), and Fungus-like Protists.
• Protists reproduce asexually (binary fission, budding) or sexually (gametes and fertilization).
• Protists are crucial in food webs, nutrient cycling, and act as symbionts or parasites.
• Alveolates include dinoflagellates, ciliates, and apicomplexans.
• Stramenopiles include diatoms, golden algae, and brown algae (kelp).
• Excavates include euglenoids and kinetoplastids.
• Rhizaria includes foraminiferans and radiolarians.
• Amoebozoans include slime molds and amoebas.
• Cilia are hair-like structures used by some protists for movement.
• Flagella are long, whip-like structures for movement.
• Pseudopodia are extensions of the cytoplasm used for movement and feeding.
• Some protists, like brown algae, are multicellular.

Fungi

• Fungi are eukaryotic, heterotrophic organisms including molds, yeasts, and mushrooms.
• Fungi obtain nutrients through absorption after secreting enzymes.
• Mycelium is the vegetative body of a fungus, composed of a network of hyphae.
• Hyphae are thread-like filaments that make up the mycelium of fungi.
• Mycorrhizae: Symbiosis between fungi and plant roots resulting in nutrient uptake.
• Chitin is the polysaccharide found in the cell walls of fungi.
• Fungi reproduce sexually and asexually through the production of spores.
• Fungi can form mutualistic relationships, such as Mycorrhizae and Lichens.
• Lichens: Symbiosis between fungi and algae or cyanobacteria.
• Mucoromycetes include common molds.
• Ascomycetes are known as sac fungi.
• Basidiomycetes include club fungi, mushrooms, and puffballs.
• Zoopagomycetes live as parasites or symbionts of animals or other fungi.
• Chytridiomycetes are primitive fungi with flagellated spores, some of which are parasitic.
• Sporangium is the structure where spores are produced.
• Lichen is a mutualistic association between a fungus and a photosynthetic partner (alga or cyanobacterium).
• Mycosis is a fungal infection.
• Many fungi are beneficial.