Physiology & Phylogenetics

Lecture 1: Introduction to Physiology & Phylogenetics

• Looks like an elongated, legless snake, but is actually a lizard
• Snakes differ in jaw mobility, vertebrae count, and tail length
• Outward appearances do not always align with close evolutionary relationships
• Limb loss evolved independently in different lizard lineages, known as convergence
• Phylogeny is the evolutionary history of a species or related group
• Explains ancestry and descent patterns
• Essential for understanding species relationships
• Binomial nomenclature consists of two parts
• Genus is capitalized
• specific epithet is lowercase
• Both are italicized, such as Homo sapiens
• Taxonomic levels increase in inclusiveness from species to domain
• Each taxon is more inclusive than the level below
• Phylogenetic trees show where lineages diverge from a common ancestor at branch points (nodes)
• The root node is the common ancestor to all taxa on the tree
• Sister taxa are each other's closest relatives, sharing a recent common ancestor
• Endpoints of branches (tips) represent present-day species or taxa
• Diagrams can be drawn in any direction without changing relationships
• Rotation around branch points doesn't alter evolutionary relationships
• The order of taxa on the right doesn't imply an evolutionary sequence or label
• Trees don't show exact ages without a time scale
• One cannot assume a group evolved “earlier” based on left-to-right arrangement
• Phylogeny can identify whale species from “whale meat” using mitochondrial DNA comparison
• Conservation efforts use phylogeny to see if species were harvested
• Homology is similarity due to shared ancestry such as forelimb bones in mammals
• Analogy is similarity due to convergent evolution, such as body forms of sharks and dolphins
• Orthologous genes are homologous genes inherited from a common ancestor, like cytochrome oxidase in humans and dogs
• Paralogous genes are from gene duplication within a species allowing functional divergence
• The molecular clock concept assesses time since divergence using genetic mutation rates
• Dating the origin of HIV from simian (SIV) to human (HIV) transmissions is an example
• Phylogenetic trees illustrate descent patterns, not physical similarities
• Classification is hierarchical
• Convergent evolution can lead to misleading similarities i.e., analogy
• Molecular data clarifies evolutionary relationships despite morphological changes

Lecture 2: Molecular Evolution, Origins of Multicellularity, Animal Body Plans

• HIV originated from simian immunodeficiency virus (SIV) transmissions
• HIV-1 M is the commonly spread strain
• Jump to humans occurred around 1930 (data suggests ~1910)
• The "Patient Zero" misconception clarified earlier virus origin
• Three domains of the tree of life include; Bacteria, Archaea, and Eukarya
• Eukaryotic genes are closer to archaea
• Horizontal gene transfer creates mosaic pattern where some genes are similar to bacterial genes
• Transfer occurs between species/domains outside vertical inheritance routes
• Multicellularity requires; cellular adhesion, cell-to-cell communication, entity individuality
• Multicellularity advantages include; defense, specialized functions, and better surface-area-to-volume ratios for exchange
• Animal characteristics include; multicellular, heterotrophic eukaryotes and a lack of cell walls
• Extracellular matrix (ECM) supports structure
• Unique tissues include; muscle for movement and nervous for conduction
• ECM components include; collagen, integrins, and fibronectin
• Collagen contains a triple-helix structure of Gly-X-Y repeats
• Integrins are transmembrane proteins bridging ECM and cytoskeleton
• Fibronectin is a glycoprotein that attaches cells to ECM
• A triple helix arrangement provides tensile strength to collagen
• Hydroxyproline formation stabilizes the helix post-translation
• Osteogenesis imperfecta results from mutations in collagen genes
• Early embryonic development goes from fertilization to blastocyst
• Zygote goes through cleavage to morula to blastula/blastocyst
• Epigenetic programming includes; global DNA demethylation early and re-established methylation patterns later
• Molecular clocks date evolutionary events like HIV emergence
• Horizontal gene transfer creates relationships
• Multicellularity needs adhesion, communication, and integration
• Early embryonic stages involve rapid cell divisions and epigenetic changes

Lecture 3: Animal Body Plans, Symmetry, Tissues and Germ Layers, Body Cavities

• Body plan elements include; symmetry, germ layers, and body cavities
• Body plan involves morphological/developmental traits that form architecture
• Radial symmetry has arrangement around a central axis
• Bilateral symmetry shows two-sided symmetry with dorsal/ventral and anterior/posterior
• Radial symmetry relates to sessile or drifting lifestyles
• Bilateral symmetry relates to active lifestyles
• Diploblastic contains ectoderm and endoderm
• Triploblastic contains ectoderm, mesoderm, and endoderm
• Ectoderm is an outer covering, sometimes nervous system
• Mesoderm is muscle, and internal organs
• Endoderm lines the digestive tract
• Coelomates have a true coelom fully lined by mesoderm
• Pseudocoelomates have a cavity between mesoderm and endoderm not fully lined by mesoderm
• Acoelomates have no coelom at all
• Functions in body cavities include, cushioning organs, hydrostatic skeleton for movement, and organ growth/mobility
• Blastopore fate in protostomes becomes the mouth
• Blastopore fate in deuterostomes becomes the anus
• Protostome examples include; Molluscs, annelids, and arthropods
• Deuterostome examples include; Echinoderms, and chordates
• Bilateria clades include, Deuterostomia, Lophotrochozoa, and Ecdysozoa
• Large animals must solve exchange challenges from the S/V ratio decreasing with size
• Strategies include; Flattening, folding, branching, and projections
• Hydra has two layers
• Large animals use complex tissues and circulatory systems
• Body plan elements reflect evolutionary solutions for structure and function
• Triploblasty leads to organs
• Protostome vs. deuterostome development is animal evolution

Lecture 4: Invertebrates & Basic Groups

• Invertebrates account for 95% of known animal species
• Occupy nearly every habitat
• Range from microscopic to meters long
• Basal animals lack true tissues with specialized cell types
• Filter feeders have pores leading to the spongocoel and exiting the osculum
• Choanocytes are flagellated collar cells driving water flow and ingesting food
• Mesohyl is a gelatinous layer between cell layers
• Spicules/Spongin provide structural support
• Cnidarians have a diploblastic, radial symmetry
• Cnidarian have a gastrovascular cavity with one opening (mouth = anus)
• Polyp forms are sessile
• Medusa forms are free-floating
• Cnidocytes and Nematocysts are specialized stinging cells with capsule-like organelles
• Lophotrochozoa have a crown of ciliated tentacles for feeding
• Trochophore larvae have a band of cilia around the middle
• Flatworms are acoelomates, unsegmented, and dorsoventrally flattened
• Have protonephridia with flame cells for excretion/osmoregulation
• Present as free-living and parasitic forms
• Flattening gives a high S/V ratio, beneficial for diffusion
• Sponges represent the branch of animals devoid of true tissues
• Cnidarians have diploblastic organization, radial symmetry, and stinging cnidocytes
• Flatworms illustrate acoelomate design, organ systems, and reliance on diffusion
• Lophotrochozoa is defined by molecular data and certain larval/feeding structures

Lecture 5: Introduction to Vertebrates, Chordate Characteristics, Fish Diversity

• Vertebrates are chordates with a backbone
• Chordate features include; flexible notochord, dorsal hollow nerve cord, pharyngeal slits/clefts, and post-anal tail
• A possible early vertebrate fossil is Myllokunmingia ~530 million years ago
• Key distinguishing features are notochord and dorsal hollow nerve cord
• Jaws evolved from modified skeletal rods of anterior pharyngeal slits
• Hox gene duplications allowed novel features
• Major groups include; Sharks & rays, ray-finned fishes, lobe-finned fishes, amphibians, reptiles, and mammals
• Chondrichthyans have a cartilaginous skeleton that is calcified, not ossified
• Adaptations include; multiple rows of teeth, spiral valve, and the ampullae of Lorenzini for electric fields
• Bony fishes (Osteichthyans) include ray-finned and lobe-finned fishes
• Ray-finned fishes have an operculum covering gills and are adapted for swim bladder buoyancy
• Lobe-finned fishes show fleshy, lobed fins with internal bone support
• Lobe-finned fishes are predecessors to tetrapods
• Gas exchange occurs with blood in the swim bladder
• Rete mirabile and gas glands regulate gas in the bladder
• Countercurrent exchange in gills maximizes O2 absorption
• Vertebrates share chordate traits plus a vertebral column
• Gnathostomes evolved jaws from pharyngeal arch supports
• Bony fishes have specialized structures enabling aquatic success

Lecture 6: Integumentary & Skeletal Systems, Cartilage and Bone in Vertebrates

• Integumentary system functions to; protect, thermoregulation, sensation, excretion, and vitamin D3 formation
• Vertebrate skin contains layers of epidermis, dermis, and hypodermis
• Gland types include; sweat and sebaceous glands
• Invertebrate integuments: Arthropods have exoskeletons, Echinoderms use ossicles, Molluscs secrete a mantle shell
• Hydrostatic skeletons include fluid-filled coelom in soft-bodied animals
• Muscles push against fluid for movement
• Exoskeletons are common in arthropods
• Exoskeletons for growth must be molted
• Endoskeletons are internal to vertebrates and grow with the organism
• Chondroblasts form cartilage, becoming chondrocytes in lacunae
• Cartilage contains flexible ECM of collagen and proteoglycans
• Cartilage heals slowly from its lack of blood supply
• Bone tissue cells include; osteoblasts, osteocytes, and osteoclasts
• Osteoblasts build bone
• Osteocytes maintain matrix
• Osteoclasts break down bone
• Osteons are concentric lamellae around a central canal
• Canaliculi connect osteocytes
• Functions include; support, movement, protection, mineral storage, and blood cell formation
• Human skeleton contains the axial and appendicular skeleton
• Integument acts as first protective barrier and has glands
• Vertebrate skeletons are endoskeletons or exoskeletons
• Bone is dynamic tissue remodeled by osteoblasts and osteoclasts

Lecture 7: Muscle Tissue, Types, and Contraction Mechanism

• Muscle tissue properties include; contractility, excitability, extensibility, and elasticity
• Muscle types in vertebrates include; skeletal, cardiac, and smooth
• Skeletal muscle is voluntary, striated, multinucleated, and attaches to bones
• Cardiac muscle is involuntary, striated, branched, and has intercalated discs
• Smooth is involuntary, non-striated, and spindle-shaped
• Muscle fiber (cell) is a long, multinucleated cell formed by fusion of embryonic myoblasts
• Hierarchy of organization includes muscle, fascicle, fiber, myofibril, and sarcomeres
• Sarcolemma is the muscle cell membrane
• T-tubules conduct action potentials into fiber from sarcolemma
• Sarcoplasmic reticulum stores and releases Ca2+
• Thick filaments contain myosin molecules with heads containing ATP-binding and actin-binding sites
• Thin filaments contain actin, tropomyosin, and troponin
• ATP hydrolysis “cocks” myosin head to form cross-bridges, power stroke occurs, ATP binds, and myosin detaches
• Repeats as long as Ca2+ and ATP are present
• Acetylcholine is released into the synaptic cleft from a motor neuron communicating
• Acetylcholine binds to trigger muscle action potential
• Action potential travels via T-tubules, SR releases Ca2+ and triggers muscle action potential
• In Myasthenia Gravis there is an autoimmune attack on ACh receptors causing muscle weakness
• In ALS there's a degeneration of motor neurons leading to paralysis
• Muscular dystrophy is a defect in dystrophin leading to sarcolemma damage
• Muscle contraction is regulated by actin-myosin cross-bridge cycling and powered by ATP
• Calcium release and reuptake control contraction/relaxation phases
• Neuromuscular disorders underscore the importance of NMJ signaling

Lecture 8: Nervous Tissue, Neuron Structure and Function, Action Potentials

• Nervous system cells include neurons are specialized for signaling and neuroglia support the environment
• Neuron functional types include sensory, motor, and interneurons
• Cell body contains nucleus & organelles
• Dendrites receive incoming signals
• Axons conduct nerve impulses and ends at synaptic knobs
• Axolemma is the axon's membrane
• Axoplasm is the cytoplasm within the axon
• Schwann cells and oligodendrocytes insulate and promote velocity
• Nodes of Ranvier are gaps in the myelin sheath where depolarization occurs
• Neurons have resting membrane potential
• Action potentials follow an all-or-none event if the threshold (~-55 mV) is reached
• Action potentials are initiated by depolarization
• Propagation is slow for Continuous Conduction
• Saltatory Conduction propagates an Action Potential faster for myelinated Neurons
• Local Anesthetics prevent numbing
• Multiple sclerosis is a neurological disorder
• Neurons rely on ion gradients and gated channels to generate signaling
• Myelin increases speed of conduction; damage causes impairments
• Action potentials follow a principle and travel long distances