Lecture 1-4 Notes: Vertebrate Zoology | PDF

Lecture 1: Introduction A. Vertebrates a. Animals with a spinal column B. Evolution a. Allows us to organize organism diversity, figure out where they originated from, and understand how they work C. Vertebrate Diversity a. 70,000 known species of extant vertebrates b. Most vertebrates are extinct, modern groups are far less diverse than they used to be c. Life is not constant through geologic time d. Cambrian explosion marked the emergence of the earliest chordates D. Taxonomy a. Established by Carolus Linnaeus b. Linnaean system → Kingdom, Phylum, Class, Order, Family, Genus, Species i. King phillip came over for good soup c. Uses binomial nomenclature i. Genus species ii. Tyrannosaurus rex → T. rex E. How evolutionary change happens a. “Descent with modification” b. Natural selection: differential survival and reproduction between individuals in a population c. Populations are the unit of evolution, not individuals d. Natural selection acts on phenotypes e. Heritable allelic variation produced by mutation is the raw material of evolution (from this, speciation can occur) F. Allopatric speciation a. Occurs when there are physical barriers to gene flow within a population b. Example: salamanders in california separated by the central valley G. Sympatric speciation a. Speciation that occurs when there is no physical barrier to gene flow b. Some persistent mechanism that prevents individuals from reproducing in the same place i. reproductive isolation follows and new species evolve c. Example: northern pacific orcas are now considered 2 different species i. Live in the same waters but do not breed or interact and have morphological differences H. Adaptive radiation a. Diversification of a group of organisms into forms filling different ecological niches b. Example: darwin and his finches I. Basic concepts of phylogenetic trees a. Each node unites tips/terminal taxa into a clade b. Clades are relative i. We are all fish, birds are dinosaurs c. Methods of classifying organisms in a tree are based on similarities shared by the included species i. Shared characteristic based on homology J. Homology vs. Analogy a. Homology: similarity between different taxa based on shared ancestry i. Example: forelimbs of humans, whales, bats, and cats b. Analogy: independent evolution of similar traits (not based on shared ancestry i. Example: dorsal fins in marine vertebrates ii. Captures convergent evolution Lecture 2: Phylogenetics and Genetic Mechanisms A. Fitness a. Some phenotypes yield better fitness in a population b. Darwinian fitness: genetic contribution of an individual to succeeding generations relative to the contributions of other members of its population i. Genotypes producing phenotypes with a higher likelihood to reproduce ii. Results in positive selection: an increase in the frequency of a genetically based trait in successive generations 1. Positive selection can lead to speciation B. Gene regulatory networks a. Gene expression can be activated or repressed via transcription factors b. Transcription factors: proteins/signalling molecules that bind to DNA and say express, don’t express, express a lot, express a little, don’t express until this time… etc c. Changing gene expression can cause a feedback loop in the original cells d. Gene families i. Genes that produce structurally related forms of the same protein ii. Developmental regulatory genes: gene families that control developmental processes 1. Examples: bone morphogenetic proteins (BMPs), Sonic Hedgehog (Shh), Gremlin e. Genes yield proteins f. Proteins dictate the phenotype which natural selection acts upon i. Example: selective breeding in bull terriers (skull and head shape via Bmp protein associated with accelerated bone growth) C. Heterochrony a. Paedomorphism: descendants retain juvenile ancestral features i. Progensis: growth stops earlier 1. Earlier onset 2. a way that small animals evolve ii. Neoteny: horns, wings, and tail grow at a slower rate 1. Reduced rate 2. a way smaller/less complex features to evolve iii. Postdisplacement: horns, wings, and tail start growing relatively later 1. Delayed onset 2. a way for later reproductive/mature development to evolve iv. Examples: adult ostriches retaining juvenile features in their heads, axolotl adults expressing juvenile traits b. Peramorphism: descendents develop “beyond” the ancestor i. Hypermorphosis: growth stops later 1. Delayed offset 2. a way that big animals and exaggerated features evolve ii. Acceleration: the horns, wings, and tails grow faster 1. Increased rate 2. a way that exaggerated features evolve like tusks and saber teeth evolve iii. Predisplacement: the horns, wings, and tails start growing earlier 1. Earlier onset 2. a way that independent young evolve D. Heterotropy a. “Different place” b. A change in the location of a gene’s expression during development c. Example: webbed feet and bat wings E. Heterometry a. “Different measure” b. A change in the intensity of a gene’s expression during development resulting in changes in the amount of the gene product (either quantity or size) c. Example: darwin’s finches → beak size controlled by a gene that yields an x amount of beak development F. Epigenetics a. Epigenetic effects: modifications of gene expression during development by non-genetic factors i. Like temperature, diet, stress, and the environment b. Can modify behavior, physiology, or morphology → phenotypic plasticity c. Types of epigenetic effects i. Intragenerational: effects limited to one generation, offspring do not inherit any phenotypic changes 1. Example: chemicals in the water causing changes in tadpoles that improve their chances of escaping predation ii. Intergenerational: effects that affect the next generation 1. Example: exposing adult stickleback fishes to predators modified the offspring’s behavior responses to predators iii. Transgenerational: effects that affect subsequent generations 1. Example: inducing postnatal stress in the mother of lab mice was documented to have extended into her grandchildren G. Cladistics a. Organisms are organized by clades b. Clades are monophyletic groups that share a single evolutionary origin and include all descendants of a common ancestor i. Common ancestor: most recent individual from which all taxa in a monophyletic group are descended c. Synapomorphies: a derived character shared by 2 or more taxa and presumed to be inherited from their common ancestor i. The characters that make a clade a clade ii. Example: upright posture for humans and mammary glands for mammals d. Apomorphy: a derived character that has changed from its ancestral state e. Plesiomorphy: characters that clade members inherited and share, but are unchanged from their ancestral state i. All clade members inherited it, but it’s not their special feature ii. Examples: humans have four limbs, and mammals have lungs, vertebrates have a vertebral column f. Synapomorphies and plesiomorphies are relative H. Understanding phylogenetic trees a. Topology: the arrangement of branches and taxa on a tree b. Sister taxa/sister group: 2 clade members that are each other’s closest relatives on a particular tree (share a more recent common ancestor) I. Paraphyly a. Referring to a named group of organisms that does not include an ancestor and all of its descendants b. Example: “fish” → all tetrapods are sarcopterygian, bony fish are derived, but “fish” also means non-tetrapod, conventional fish J. Types of characters a. Molecular i. Compares all life ii. Directly based on genotype iii. Better for more recent evolutionary divergences, harder for older things iv. Functional significance of DNA differences can’t always be seen v. Homoplasy (independent evolution of a similar trait) can occur b. Morphological i. Easy to obtain ii. Can be applied to the fossil record iii. Phenotypic plasticity (variation within the same species) is a disadvantage iv. Ambiguously defined v. Continuous and not discrete vi. Easier for older things (like in rock layers) K. Merging genetics and phylogeny a. Example: spots of a panthers coat i. Ancestors probably had some types of spots, lions can be expressing some type of heterochrony where spots turn off as they age, and tigers may be experiencing some type of heterometry where spots are ultra-expressed, resulting in stripes Lecture 3: What’s a vertebrate? A. Directional terms a. Axial skeleton: vertebrae, ribs, spinal column, median fins b. Appendicular skeleton: pectoral and pelvic girdles, associated fin or limb bones c. Cranial skeleton: skull and jaw d. Postcranial skeleton: everything else B. Vertebrate plesiomorphies a. Heterotrophs b. Bilateral symmetry c. Triploblastic i. Ectoderm: outermost layer 1. Forms superficial layers of the skin, linings of the digestive tract, and most of the nervous system ii. Mesoderm: middle layer 1. Forms the muscles, skeleton, deeper layers of the skin, connective tissues, circulatory system, kidneys 2. Develop in a segmented fashion from anterior to posterior iii. Endoderm: innermost layer 1. Forms rest of digestive system, portions of urinary system, gills and lungs, taste buds, germ cells (gametes) iv. Gastrulation: movement of undifferentiated cells of the early embryo into these 3 layers d. Coelom i. Body cavity that contains internal organs like the heart and gut tube ii. Divided into… 1. Pericardial cavity: contains the heart 2. Peritoneal cavity: contains the GI tract, liver, pancreas, gallbladder 3. Both are separated by the transverse septum iii. Divisions get more complex in more derived vertebrates to accommodate lungs → Pleural recesses iv. Coelomic cavities are lined by thin sheets of mesoderm… 1. Pericardium: on surface of the heart and lining the pericardial cavity 2. Peritoneum: in the peritoneal and pleural cavities e. Blastopore: original opening of embryonic gut formed during gastrulation i. Protostomes: blastopore becomes mouth ii. Deuterostomes: blastopore becomes anus (vertebrates) f. Chordates C. Chordate synapomorphies a. Notochord i. Dorsal stiffening rod ii. Attachment for swimming muscles b. Dorsal neural tube i. Coordinates muscle activity for swimming c. Muscular post anal tail i. Provides more swimming power d. Endostyle i. Glandular groove on the pharynx (throat) ii. Homologous to thyroid iii. Secretes mucus for trapping food particles for filter feeding iv. Takes up iodine D. Chordate organization vs. non chordate organization a. Annelids (worms) and chordates have flipped locations of their nerve cord and their heart → an example of heterotropy E. Extant nonvertebrate chordates a. Lancelets (cephalochordata) i. Not the sister group to vertebrata despite retaining all ancestral chordate characters b. Tunicates (urochordata) i. Sister group of vertebrata ii. Quite derived → larvae become non-moving, lose post-anal tail, and reduce the neural tube F. Vertebrate synapomorphies a. Vertebrae i. Support, protection, locomotory muscle origins ii. Cartilaginous or bony b. Cranium i. “Brain case” → bone, cartilaginous, or fibrous structure surrounding brain c. Head, sense organs, tripartite brain i. Tripartite: forebrain, midbrain, hindbrain to integrate sensory info d. Complex endocrine organs i. Produce hormones to regulate body functions e. Muscularized gut tube i. Muscles in the wall of the gut tube for processing of large amounts of food f. Multichambered heart i. Distributes gases and nutrients to all cells of the body g. Mineralized tissues i. Calcium deposits in tissues ii. Calcified cartilage and bone as well as teeth (dentine, enamel, etc) h. Gills derived from endoderm i. Efficient respiration i. Neural crest i. differentiation j. W-shaped myomeres i. Produce lateral undulations for swimming in fish ii. Six-pack G. Chordate and vertebrate homology a. Chordate characters: In vertebrates: Notochord Replaced by vertebral column and remain as intervertebral discs in the spine Neural tube Becomes central nervous system Postanal tail Tails in vertebrates that have them Endostyle Thyroid H. Development of pharyngeal region a. Pharyngeal arch: segmentally organized tissues between the gill slits b. Derivatives of the pharyngeal arches are strongly conserved through vertebrate history (just changed to do different things → gene expression) c. Pharyngula: developmental stage in vertebrate embryos characterized by the presence of pharyngeal arches and slits d. Pharyngeal arch #2 and #3 contribute to the hyoid bone e. Arch #1 associated with bones in the ear and muscles of mastication f. Mammals don’t have a 5th arch, it was lost I. Development of the brain a. Neural plate: early embryonic structure that gives rise to neural tube i. Evolved into neural tube (chordates): precursor to CNS, primary neuron generating tissue 1. Evolved into the forebrain, midbrain, and hindbrain 2. Forebrain: olfaction 3. Midbrain: vision 4. Hindbrain: motor functions, respiration, circulation J. Neural crest a. Embryonic tissue that gives rise to unique structures in vertebrates like neurogenic tissues (tissues giving rise to neurons) b. Perhaps the most important innovation in the vertebrate body plan c. Sometimes considered a 4th germ layer d. Neural crest cells are migratory and versatile K. Neurogenic placodes a. Thickenings in the embryonic ectoderm that give rise to nerves and sensory receptors of the nose, ear, and other sensory systems b. Migrate c. Others are not neurogenic and give rise to structures like feathers and hair L. Why did vertebrates evolve??? a. Vertebrate characteristics are far more powerful and efficient in… i. Feeding ii. Respiration iii. Locomotion b. Remember the food tube M. Evolution of bone tangent a. Bones evolved as mineral storage to “act like batteries” b. They would store minerals and later release them as needed and rebuilt, they just happened to turn into internal protective mechanisms and rigidifying structures along the way c. Important to convince your body that you need that bone for more than just storage (weightlifting super important) N. Integumentary system a. Protection, regulation of body temp, sensation, communication b. Epidermis c. Dermis i. is unique to vertebrates ii. Derived from mesoderm and neural crest d. Hypodermis i. Connective tissue layer anchoring the skin to muscles and organs ii. Also unique to vertebrates O. Cranial skeleton a. Dermatocranium i. Bones that cover a portion of the skull ii. Protect brain, anchor teeth, provide muscle attachment sites iii. Forms from neural crest and mesoderm b. Chondrocranium i. Surrounds the brain ii. Forms from neural crest and mesoderm c. Splanchnocranium i. Forms from neural crest and contributes to jaws, jaw support, and gills P. Circulatory system a. Arteries: carry blood away from the heart i. Blood pressure higher than in veins b. Veins: carry blood back to the heart c. Capillaries: smallest vessels, sites of exchange of gases, nutrients, and waste products between blood and tissues d. Ancestral vertebrate heart has 3 chambers i. Sinus venosus: receives blood from veins ii. Atrium: intermediate place for blood iii. Ventricle: applies for to eject blood Lecture 4: Cyclostomes and Gnathostomes A. Obtaining oxygen from water using gills a. Gills: vascularized (full of blood) structures where O2 and CO2 are exchanged between the body and surrounding water b. Internal gills: consist of primary lamellae (gill filaments) i. Your classic gills ii. Secondary lamellae: microscopic projections from primary lamellae where gas exchange occurs c. External gills: some fish and amphibians have this, they are attached to the sides of the head i. Axolotls have this d. Water flow in unidirectional (unlike lungs) B. Types of gill ventilation a. Buccopharyngeal (buccal) pumping: drawing in air or water into the mouth and pharynx and expelling it i. More ideal b. Ram ventilation: where a respiratory current across the gills is generated by fish swimming with its mouth open i. Used by filter feeders and open ocean fish including tuna, mackerel, swordfish, and some sharks c. Many fish use both, buccopharyngeal pumping at rest and ram ventilation when swimming C. Gas exchange a. Countercurrent exchange: when the direction of blood flow through the secondary lamellae is opposite to the direction of water flow i. Max O2 absorption ii. Like when basketball players say good game at the end of a tournament b. Many fish breathe air via lunds or other structures c. Lungs evolved in fish and precede the evolution of tetrapods by millions of years i. Likely evolved in active fish to supply additional oxygen ii. Then co-opted for breathing in stagnant environments and eventually in tetrapods D. Buoyancy a. Neutral buoyancy: density equal to water, neither sink or float (hovering) i. Many actinopterygians (mostly teleost) ii. Made possible by a gas bladder (swim bladder): air filled organ used to regulate buoyancy 1. 5% body volume in marine teleosts and 7% in freshwater teleosts because saltwater environments are more dense which makes you more buoyant (their swim bladders can take up less space) b. Negative buoyancy: density greater than water (sink) i. Bottom dwellers) c. Positive buoyancy: density less than water (float) d. Physostomous fish i. Pneumatic duct: connection between the gas bladder and gut ii. These fish can gulp air at the surface to fill the bladder and burp gas out to reduce bladder volume 1. Present in basal teleosts like eels, herring, anchovies, minnows, and salmon e. Physoclistous fish i. Derived teleost fish where adults lack pneumatic duct ii. They increase the volume of gas bladder by secreting gas from the blood into the bladder, then decrease volume by absorbing bas from the bladder and releasing it through the gills 1. Rete mirabile (“wonderful net”): moves O2 from blood into gas bladder iii. To release excess gas they open a sphincter muscle to allow gas to enter the ovale 1. Diffuses oxygen into the blood f. Cartilaginous fish i. Sharks, rays, and chimaeras do not have a gas bladder, they use… 1. Nitrogen containing compounding in the blood and muscle tissue (urea) 2. Their livers a. High oil content i. Oil is lighter than water so it helps them float b. A bottom dwelling shark would have a less oiler liver compared to a shark that lives closer to the water’s surface E. Sensory a. Vision i. Air refraction index= 1.00 ii. Water refraction index= 1.33 iii. Vertebrate cornea refraction index= 1.37 iv. The refractive index of the cornea is too close to that of water which is why our vision is blurred v. Aquatic vertebrates have a spherical lens with high refraction which helps them see clearly underwater b. Olfaction and taste i. Jawed fish 1. Have paired nasal sacs 2. Water flows into the incurrent nostril, over the olfactory space in the nasal sac, and out through the excurrent nostril (unidirectional) ii. Lampreys 1. Single median nostril 2. Moves water in and out 3. They smell the way we breathe c. Detecting water displacement i. Hair cells detect the motion of fluids 1. Form neuromast organs: clusters of sensory hair cells ii. Lateral line system: sensory system on the body surface of fish and aquatic amphibians that detects water movements 1. Found only in aquatic vertebrates because air is not dense enough to trigger neuromast organs d. Hearing i. Hair cells also function in hearing where they respond to sound waves ii. Sound travels faster in water because it goes precisely from water molecule to water molecule, uninterrupted iii. Sound reaches and stimulates by several routes 1. Chondrichthyians and osteichthyans a. Sound travels through tissues of the skin and skull to reach the inner ear b. Don’t have an ear hole and lots of resolution is lost 2. Osteichthyans with gas bladders a. Sound travels through tissues to the gas bladder, which then vibrates in resonant frequency to be transmitted to the inner ear b. Can detect high frequency sound this way 3. Some osteichthyans a. Catfish, minnows, goldfish b. Vibrations that reach the gas bladder are transmitted to the inner ear by small bones called Weberian ossicles c. These fish are even more sensitive to high frequency sound d. Most efficient e. Electroreception i. Passive electroreception: ability to detect weak electric fields generated by muscle contractions of aquatic prey 1. Water conducts electricity ii. Animals with passive electroreception can detect prey with electroreceptors called ampullary organs (ampullae) 1. Filled with electrically conductive gel 2. Universal among chondrichthyans who use it to detect and capture prey iii. Ampullae of Lorenzini: on the head and are most concentrated in front of the mouth where they help direct the “final strike” at a prey animal F. Homeostasis a. Tendency of an organism to maintain a stable internal state b. Achieved via osmoregulation and thermoregulation i. Osmoregulation: process of maintaining both water and salt balance so that body fluids do not become either too dilute or too concentrated 1. Organism = leaky bag of dirty water 2. Exchanges of matter and energy with the environment are essential to survival 3. Osmosis: movement of water across a semipermeable membrane from a dilute solution to a more concentrated solution a. Isosmolal: same solute concentration as water i. No osmosis ii. Hagfish b. Hyposmolal: lower solute concentration inside the body than the surrounding water i. Marine teleosts 1. Water and salt balance constantly threatened by outflow of water and inflow of ions ii. Water flows out from body into surrounding water c. Hyperosmolal: higher solute concentration inside the body than the surrounding water i. Sharks and freshwater fish 1. Must cope with inflow of water and outflow of ions ii. Water flows into their bodies G. More on osmoregulation a. Most fish and lissamphibians are stenohaline: inhabit either seawater or freshwater and tolerate only modest changes in salinity (sensitive) i. Marine shark → hyperosmolal in seawater ii. Marine teleost → hyposmolal in seawater iii. Freshwater teleost → hyperosmolal in freshwater b. Some fish and lissamphibians are euryhaline: they migrate between freshwater and seawater and tolerate large changes in salinity i. Anadromous: fish that move from seawater to freshwater to reproduce 1. Atlantic salmon ii. Catadromous: fish that move from freshwater to seawater to reproduce 1. American eel H. Earliest Vertebrates a. Haikouichthys I. Origin of vertebrates a. 3 lines of evidence support the hypothesis of a marine origin of vertebrates i. Earliest fossils found in marine sediment ii. Invertebrate deuterostomes are exclusively marine and are isosmolal iii. Hagfish have concentrated body fluids like surrounding seawater J. Cyclostomata a. Extant jawless vertebrates b. Clade that includes hagfish and lampreys c. Characters that separate them from gnathostomes i. Single median nostril ii. Branchial basket (simple gills) 1. Unarticulated gill arch 2. In gnathostomes, the gill arch has joints between iii. Gill arch lateral (outside of) to the gill tissue 1. In gnathostomes, the gill arch is medial (inside of) to gill tissue iv. Velum: membranous flap in the pharynx moved by muscles to pump water over gills v. Tongue that bears keratinous teeth and is supported by cartilage 1. Cyclostome tongue not homologous to gnathostome tongue K. Hagfish (Myxiniformes) a. All marine b. Deep, cold water habitats and are scavengers of the sea floor c. Drawn to carcasses by their sense of smell d. Have keratinized teeth arranged front to back and close in the horizontal plane (unlike the jaws of gnathostomes that open and close in the vertical plane) e. Median nostril used to take in water for olfaction and gill ventilation f. Pharynx and gill slits are behind (posterior) the head g. Only extant vertebrates with a pre-anal fin L. Lampreys (Petromyzontiformes) a. Sister clade to hagfish b. Shared characters (synapomorphies) of lampreys include… i. Seven pairs of gill pouches ii. A round mouth located at the bottom of the buccal funnel c. The nostril does not connect to the oral cavity or pharynx like it does in hagfish d. The eyes are well developed with good color vision M. Cambrian vertebrates a. Cambrian vertebrates and extant cyclostomes lack mineralized tissue (they are mostly made of cartilage) N. Gnathostome synapomorphies a. Joints between skeletal elements of gill arches i. Allow double-pump gill ventilation (expand and suck) which results in large volumes of water moving across the gills to enhance the exchange of gases b. Jaws with true teeth (dentine and enamel) c. 2 dorsal fins d. A set of pectoral and and pelvic fins e. Segmental W- shaped axial muscles O. Hox genes and gnathostome evolution a. Hox genes: a group of control genes that determine the body plan of an animal during embryonic development (decides which body parts go where) b. All animals have hox genes, but vertebrates have more hox gene clusters than other animals i. All extant vertebrates have 2 clusters of hox genes resulting from a duplication of the single hox gene complex in nonvertebrate chordates c. Eugnathostomata (the group that includes chondrichthyes and osteichthyes) have 4 clusters of hox genes resulting from a second duplication i. Resulted in more refined genetic control of development leading to more anatomical possibilities P. Why jaws?? a. Why modify mandibular cartilages into a biting apparatus when you already have mouth parts? b. Ventilation hypothesis: jaws would have allowed early gnathostomes to suck in larger volumes of water → improving respiration and gas exchange Q. Evolution of paired appendages a. So they can spin (roll), move side to side in a circle (yaw), and do front flips (pitch) b. Better thrust and acceleration Lecture 5: Chondrichthyans and Osteichthyans A. Living gnathostomes include chondrichthyes and osteichthyes B. Chondrichthyans a. Cartilaginous “fish” b. Elasmobranchii is one chondrichthyan clade that has extant members C. Elasmobranchii a. Extant elasmobranchs are solely in the clade Neoselachii which includes extant Selachii (sharks) and Batomorphi (rays and skates) i. 2 clades of extant selachians 1. Galeomorphii a. “Famous” sharks → hammerhead, whale shark, great white 2. Squalomorphi a. Generally smaller than galeomorphs b. Spiny dogfish ii. Batomorphii 1. Skates → Rajiformes 2. Rays→ Myliobatiformes 3. Primarily bottom dwelling 4. Flattened teeth, mouth is extremely protrusible providing powerful suction to dislodge shells from prey 5. Skates vs. rays a. Skates have a circular body outline with a strong rostrum whereas ways are diamond shaped b. Skates have 2 dorsal fins and terminal caudal fin and are oviparous (lay eggs) c. Rays have a whiplike tail and the fins are replaced by one or more elongated, serrated, and venomous dorsal barbs i. They are also viviparous, giving birth to live young D. Euchondrocephalii a. Sister clade to Elasmobranchii b. Include Holocephalii and Chimaeriformes c. Chimaeriformes are the only extant members of Euchondrocephalii E. Characters of Chondrichthyans a. Placoid scales composed of dentine and enamel i. Reduce drag during swimming and help to resist abrasion b. Cartilaginous skeleton i. Their skeletons are mineralized with the same mineral as osteichthyans use in their bones, but chondrichthyans deposit the mineral differently, forming calcified cartilage ii. They lost bone in their evolution c. Internal fertilization i. Males have pelvic claspers used to channel sperm into the female’s cloaca ii. Some are oviparous (ancestral) and some are viviparous d. Chondrichthyan teeth i. Form tooth whorls 1. Continually replaced as they wear and are lost 2. Tooth shape tells us about rolls in feeding: tearing, cutting, and crushing F. Shark sense integration and hearing a. Olfaction b. Mechanoreception (from lateral line) c. Vision d. Electroreception (via ampullae of Lorenzini) and mechanoreception e. Swimming i. Caudal fin shape reflects environment G. Elasmobranch brains a. Have larger brains for more sensory, motor, and interneurons than smaller animals H. Osteichthyes a. All extant vertebrate groups other than cyclostomes and chondrichthyes are osteichthyans b. The 2 clades of osteichthyes are Sarcopterygii (flesh/lobe-finned fish which encompasses tetrapods) and Actinopterygii (ray-finned fishes) I. Actinopterygian vs. Sarcopterygian fins J. Osteichthyan characters a. Internal skeleton with ossified bones b. Gas containing lung i. Derived from embryonic gut used for breathing c. Many dermal bones in their heads i. Opercular bone that covers the gills and aids in gill ventilation d. Dermal bones that form the palate and bear teeth e. Fin rays f. Ancestral enamel: shiny, enamel like tissue on scales and dermal bones i. Evolutionary precursor to true enamel K. Actinopterygians a. A clade within osteichthyans b. Most extant actinopterygians are teleosts L. Actinopterygian clades a. Polypteriformes i. Most basal extant actinopterygian ii. Diphycercal caudal fin iii. Series of dorsal finlets instead of a single dorsal fin (kinda looks like the spikes on a stegosaurus) b. Acipenseriformes i. Sharply asymmetrical heterocercal caudal fin ii. Sturgeons and paddlefish c. Holostei i. Abbreviated heterocercal caudal fin ii. Sister group to teleost, both are included in neopterygii iii. Includes lepisosteiformes (gars) and amiiformes (bowfin) d. Teleosts i. Homocercal caudal fin Lecture 6: Actinopterygians A. Most actinopterygians are teleosts B. Teleost characters a. Homocercal caudal fin b. Oral jaws i. Bony elements that surround the mouth opening ii. May or may not have teeth c. Pharyngeal jaws d. Scales i. Lack ganoine ii. Much thinner layer of bone than non-teleosts iii. Together, these thinner scales make the teleost body more flexible for swimming than that of a gar iv. More basal teleosts have round, cycloid scales while more derived teleosts have ctenoid scales e. Swimming i. Gas bladders for buoyancy regulation ii. The skeleton of the paired fins became simplified → primarily fin rays iii. These paired fins are used for social signaling, courtship, braking during swimming… etc f. Reproduction i. Pelagic eggs: float freely in the water C. Teleost clades a. Elopomorpha i. Tarpons, bonefish, ladyfish, true eels ii. All but few are marine iii. Share leptocephalus: a kind of larval stage where they spend a long time drifting near the surface where they can be widely dispersed by currents b. Otophysi i. Carps, minors, piranhas, catfish, electric eels ii. Weberian apparatus 1. Connects the gas bladder to the inner ear allowing for high frequency pick up (very sensitive to sound) c. Euteleosti i. Dragonfish→ most abundant ii. Lanternfish iii. Cods and allies → most important wild-caught commercial fish d. Acanthopterygii (percomorpha) i. Seahorse, barracuda, billfish, flounder, halibut D. Swimming and hydrodynamics a. Strong correlation between a fish’s body length and its swimming speed i. Longer fish swim faster E. Actinopterygian reproduction a. Most diverse in reproduction than any other vertebrate group b. Oviparity i. Most ray-finned fish are oviparous ii. Freshwater→ generally produce relatively small number of large, yolk rich eggs, which they bury in gravel or place in a nest or attach to the surface of a rock (in contrast to pelagic eggs) iii. Marine→ usually large numbers of small, buoyant, transparent, pelagic eggs are released to float in the water column c. Viviparity i. Guppies d. Can change their sex (in teleosts) F. Actinopterygian ecology a. Photic zone: most of the biomass occurs here (top 1000m of water) i. Alltiphotic: very most top layer 1. Coral reef fishes 2. Very diverse 3. Almost all vertebrates that live on reefs are teleosts ii. Mesophotic: iii. Rariphotic: b. Pelagic and deep-sea fish (basic ocean) i. Light levels in epipelagic (top 200m) can support photosynthesis, so oceanic biomass is concentrated in the epipelagic and mesopelagic (“twilight zone”) beneath it ii. Food webs in ocean depths rely on falling detritus iii. Below the mesopelagic is the bathypelagic (it is dark and cold) c. Epipelagic fish i. Sardines, herring, tuna ii. Countershading in pelagic predators d. Mesopelagic teleosts i. Daily vertical migrations ii. During the nighttime, they come up to the epipelagic zone to feed, but once it gets light out, they return to the mesopelagic zone to avoid predation 1. Higher productivity at night (food is more concentrated so they can gather more energy) 2. Shallower water is warmer so their metabolic rates increase and they use energy faster 3. Daytime descent into cooler water lower metabolism and conserves energy e. Bathypelagic teleosts i. Have large mouths to engulf nearly anything and large stomachs to accommodate any meal 1. Do not travel because it is too far and too much energy Lecture 7: Sarcopterygians A. Sarcopterygians a. What we are b. Flesh/lobe finned “fish like” fish and tetrapods → amphibians, lizards, birds, and mammals c. Within osteichthyes d. Sister clade of actinopterygians B. “Fish like” sarcopterygians a. Actinistia → Coelacanthiformes b. Dipnomorpha → lungfish (neoceratodontidae and lipdosirenidae) C. Crown tetrapods a. Crown group: composed of all living representatives of the collection, the most recent common ancestor of the collection, and all descendents of the most recent common ancestor i. Members of a crown group have all of the derived characters of the extant members of a clade b. 3 clades of sarcopterygians are extant with more than 99% of the species in tetrapoda D. Sarcopterygia phylogeny a. Coelacanthiformes and dipnomorpha are not sister clades b. Coelacanthiformes are the most basal sarcopterygian and branch off first c. Dipnomorpha (lungfish) are the sister group to tetrapods E. Sarcopterygian synapomorphies a. Presence of the hard tissue cosmine on dermal bones and scales i. Composed of dentine and enamel and found on bones and scales b. Monobasic paired fines with a scaled, muscular lobe at the base i. Precursor to humorous c. An intracranial joint between the anterior and posterior portions of the braincase i. We no longer have this F. Coelacanthiformes a. In the clade actinista b. Have a long and excellent fossil record G. Coelacanthiform characters a. 3 paired openings of the rostral organ b. Specialized receptive organ (unique to this animal) c. Paired fins and a second dorsal and anal fin with muscular, lobed bases d. Diphycercal caudal fin with terminal tuft H. Coelacanthiform physiology a. Latimeria resemble chondrichthyans in retaining urea to maintain a blood osmolality close to that of seawater b. The lung of extant coelacanths is vestigial i. The fat fill lung of Latimeria serves as a buoyancy organ but no function of gas exchange I. Coelacanthiform reproduction a. Viviparous→ give birth to large, fully formed pups b. Internal fertilization must occur but how copulation happens is unknown because males lack an intromittent organ J. Coelacanthiform ecology a. Live in the photic zone i. Explains the absence of coelacanths from the fossil record because these habitats rarely yield well preserved fossils b. Latimeria chalumnae is nocturnal, hiding in caves during the day and venturing out at night to dine on small fishes, squids, ad octopuses i. Swim with their pectoral and pelvic fins in diagonal pairs, just as tetrapods move their limbs on land (kinda walky swimmy thingy) K. Dipnoi a. Use both gills and lungs b. 3 extant genera remain i. Neoceratodus → Australia ii. Lepidosiren → South America iii. Protopterus → Africa L. Dipnoi synapomorphies a. Reduction and loss of outer dental arcade (the tooth bearing maxilla, premaxilla, and dentary bones) aka they lost oral jaws b. Fusion of 2 bones in the cranium M. Dipnoi structural characteristics a. Lungs with small chambers for gas exchange (sort of like alveoli) b. Partially divided atrium in the heart and pulmonary vein that delivers oxygenated blood to its left side c. Mix of sensory organs with some associated with living on land and some with living in water i. Large olfactory organs for smell and taste ii. Lateral line system that detects water currents iii. Ampullary receptors concentrated on the snout N. The Australian Lungfish a. Neoceratodus forsteri can have long lifespans and grow to 1.5m long b. Omnivorous c. Uses well developed gills for gas exchange and although it can use it’s single lung to obtain oxygen, it does not depend on air breathing d. Has a massive genome, about 14 human genomes put together (largest known for any animal, about 43Gb) O. South American and African lungfishes a. Lepidosiren (South America) and Protopterus (African) have… i. Paired lungs ii. Long, eel-like bodies iii. Threadlike paired find with reduced internal skeletons (sort of like catfish whiskers) b. They have comparatively reduced gills but derived all of their oxygen from them c. One giant muscle tube basically so they are really good swimmers d. The african lungfish (Protopterus) dig a vertical burrow into the mud during dry season and surround themselves in a mucus like layer and essentially hibernate until conditions get better (wetter) e. Why have gills and lungs then??? i. It is easy to lose carbon dioxide to the surrounding water through gills, so the African and South American lungfish can partition gas exchange between lungs and gills P. The first tetrapods a. Come from late devonian period (about 360 million years ago) b. Were primarily aquatic rather than terrestrial Q. Crown tetrapods a. During the early Carboniferous, crown Tetrapoda diversified into clade like Lissamphibia and Amniota b. Time in history called Romer’s gap where fossil records from that time are scarce R. Challenges of living on land a. Body support b. Locomotion c. Eating d. Breathing air e. Conserving water f. Circulation g. Sensory S. Structural differences between tetrapodomorph fish and an early tetrapod (limbs) a. In fish and tetrapodomorph fish i. Pectoral girdle attaches to the posterior portion of the skull, so there is no flexible neck ii. The pelvic girdle is embedded in muscle; so its not attached to the vertebral column b. In Devonian tetrapod i. The pectoral girdle does not attach to the skull which means there is a flexible neck ii. The pelvic girdle attaches to the vertebral column which helps support body weight T. Structural differences between tetrapodomorph fish and an early tetrapod (vertebrae) a. The vertebral column in tetrapods resists compression, torsion, and the pull of gravity b. Zygapophyses: projections on the vertebrae that allow adjacent vertebrae to fit together i. So that the vertebral column can support the body and resist torsion ii. The ribs also articulate to allow the vertebral column to transfer weight of the body to the limbs U. Support on land a. Tetrapod hypaxial muscles evolved modifications to resist torsion and stabilize the trunk because of the pull of gravity on land b. Tetrapods use muscles for body support as well as for locomotion, and they are bolstered by internal connective tissue making tetrapod muscles tougher to cut than flesh of fishes i. Ribs of the earliest tetrapods were also much more robust than the ribs of a fish V. Body supporting limbs a. The limb elements of Devonian tetrapods preserve the monobasic arrangement that is synapomorphic for all sarcopterygii i. Stylopodium: humerus in the forelimb and femur in the hindlimb ii. Zeugopodium: the radius and ulna in the forelimb and the tibia and fibula in the hindlimb iii. Autopodium: the wrist, hand, and digits in the forelimb, and the ankle, foot, and digits in the hindlimb b. Our limbs are advanced fins c. How did fins become limbs?? i. Hox genes ii. Heterometry→ amount of gene expression in development coding for less development (no fin shape) W.Eating on land a. On land, its harder to get food into your mouth and down your throat b. The tongue is a major innovation for terrestrial feeding i. Large, muscular, and mobile ii. Some (salamanders and lizards) even use sticky or projecting tongues to capture prey and transport it into the mouth X. Circulation on land a. Circulation is much more difficult in terrestrial vertebrates because blood must be pushed uphill into portions of the body that are higher off the ground than the heart (pooling must also be prevented) i. As a result, blood pressure is higher in terrestrial vertebrates b. Tetrapods have double circulation in which the pulmonary circuit supplies the lungs with deoxygenated blood and the systemic circuit supplies the body with oxygenated blood i. Oxygenated blood from the lungs returns to the heart to be pumped to the rest of the body c. Single circulation: in fish were oxygenated blood from the gills flows straight to the body without first returning to the heart Y. Senses on land a. Vision i. Refractive index of the cornea is greater than that of air, so in air, the cornea participated in forming a focused image (as opposed to the spherical lens in water) b. Olfaction i. Tetrapods have 2 chemosensory systems… 1. Main olfactory system a. Used to detect volatile odorants (airborne/evaporants) b. Located in the nasal passages (very sensitive) c. Tetrapods couple olfaction and respiration (need to breathe to smell) 2. Accessory olfactory system a. Used to detect nonvolatile odorants (ones that are less likely to disperse in air) b. Lost in several groups c. Based on the vomeronasal organ unique to tetrapods in the anterior roof of the mouth d. Unlike the main olfactory system where air passes as it is inhaled, the vomeronasal organ is a pouch in the mouth i. Flehmen behavior Z. Origin of Lissamphibia a. Lissamphibians are separated into Stereospondyli and Dissorophoidea which gave rise to extant lissamphibians like salamanders and frogs b. Dissorophoidea i. Frogs (anura) and salamanders (caudata) are both in the clade batrachia and are the only extant members of dissorophoidea c. Stereospondyli i. Caecilians (gymnophiona) are the only extant members Lecture 8: Lissamphibians A. Synapomorphies a. Moist, permeable skin i. Evaporate water quickly in dry conditions but absorb water from wet surfaces and moist soil b. Substantial cutaneous gas exchange i. Breathe through their skin c. Skin glands i. Mucus embedded in the skin help maintain their moisture d. Carnivory i. Will eat everything and anything e. Columella operculum complex i. 2 bones that transmit sound to the ear 1. Columella→ transmits high frequency sounds to inner ear 2. Operculum→ transmits low frequency ground vibrations a. Not homologous to the operculum in fish f. Structure of the levator bulbi muscle i. Causes the eyes to bulge outward, thereby enlarging the buccal cavity (oral cavity) g. Green rods i. “Red rods” found in all vertebrates that are sensitive to green light ii. Green rods help with sensitivity to violet and blue light, making them see better at night 1. At night, the light shifts towards blue (some frogs look different at night than the do in the day like the red-eyed tree frog) iii. Skin fluorescence is also widespread among lissamphibians B. Other senses in lissamphibians a. Aquatic larvae of lissamphibians and adults of permanently aquatic species have a lateral line system homologous to that of bony fish b. Electroreception based on ampullary organs i. Entirely absent in frogs but present in aquatic larvae of caecilians and salamanders C. Caudata a. Most entirely limited to the northern hemisphere b. Nearly ⅔ of extant salamander species are plethodontids c. The eastern US has the highest salamander diversity in the world D. Salamander ecology a. Love caves because of rotting things like insects (dampy and swampy) b. Tongue projection i. Have specialized projectile tongues that can travel a significant distance from the mouth to capture prey E. Salamander families and features a. Hellbenders (cryptobranchidae) i. Big ones, paedomorphic, aquatic b. Sirens (sirenidae) i. Elongated aquatic with external gills, lack pelvic girdle and hindlimbs c. Mole salamanders (ambystomatidae) i. Similar to large terrestrial salamanders with aquatic larvae d. Mudpuppies (Proteidae) i. Paedomorphic aquatic salamanders with external gills e. Amphiumas (amphiumidae) i. Elongated aquatic salamanders lacking gills f. Lungless salamanders (Plethodontidae) i. Aquatic or terrestrial, some with aquatic larvae, others with direct development F. Salamander reproduction a. No male/female contact i. Males transfer a packet of sperm that the female take up to fertilize her eggs b. In most cases, salamanders that breed in water lay their eggs in water i. They hatch into gilled aquatic larvae (except in permanently aquatic species) and transform into terrestrial adults c. Some families (primarily plethodontidae) include species that have gotten rid of the aquatic larval stage i. But some don't = speciation!!! d. Only a few species are viviparous e. Paedomorphosis i. Paedomorphic individuals do not undergo metamorphosis and instead retain their larval form (gills, lateral line, electroreceptive systems, and aquatic habitat) ii. Some species are facultative paedomorphs that typically metamorphosize but under certain environmental conditions will remain in the larval state (epigenetics) G. Caecilians are equally related to anything in batrachia (frogs and salamanders) H. Anurans a. Frogs and toads I. Body form and locomotion of Anurans a. Specialization of the body for jumping (but not always) b. The hindlimbs form a lever system that can catapult the animal into the air i. Elongated hindlimbs with tibia and fibula fused ii. Powerful pelvis strongly fastened to the vertebral column iii. Elongated ilium iv. Urostyle v. Short vertebral column that resist torsion via zygapophyses vi. Strong forelimbs and flexible pectoral girdle c. Anuran jumping ability varies from hoppers to leapers i. Short legged species move by hopping 1. Have potent defense mechanisms ii. Species that move by jumping or leaping 1. Usually sedentary predators that wait and ambush J. Anuran tongues a. Sticky b. Use a catapult like system to project the tongue and aquatic species use suction to engulf food K. Why do anurans look like that?? a. Probably evolved from a salamander-like starting point b. Some propose that their body form evolved because of the advantages of using the hindlimbs for swimming (burst ability) L. Anuran families and features a. Treefrogs (Hylidae) i. Largest clade ii. Mostly tree frogs but some are aquatic and terrestrial b. True toads (Bufonidae) i. Mainly short-legged and terrestrial ii. Most have aquatic larvae c. True frogs (Ranidae) i. Large clade of aquatic and terrestrial frogs ii. Most have aquatic tadpoles M. Anuran reproduction a. Frog vocalizations i. Mating calls but also advertisement (competition) calls ii. Can also supplement or replace calls with visual signals b. Mating systems are divided into… i. Explosive breeding 1. Breeding season very short, sometimes only a few days 2. Use temporary aquatic habitats like tiny pools ii. Prolonged breeding 1. Breeding seasons may last for several months 2. Males usually arrive first and establish territories that they defend for a long time N. Anuran metamorphosis a. The gills, lateral line, and electroreceptive systems are lost; eyelids, skin glands, and adult teeth appear b. For anurans, the process by which an aquatic tadpole becomes and adult frog requires complete metamorphosis i. Tadpole structures are broken down and their chemical constituents are completely rebuilt O. Gymnophiona (caecilians) a. Terrestrial, very few aquatic b. The eyes are greatly reduced and covered by skin or bone c. Have dermal scales d. Kinda look like millipede snakes P. Gymnophiona derived character a. Solid roofed skulls b. Dual sets of jaw-closing muscles are a unique character c. Have little tentacles i. Associated with the eyes ii. Also could be a sensory organ (sort of like the vomeronasal organ) iii. They feed on small prey (termites, earthworms, insects) Q. Gymnophiona reproduction a. Fertilization via the male intromittent organ b. Parental care → mom curls up with the eggs and stays until they hatch c. Some oviparous species have direct development, but viviparity is widespread d. Dermatophagy: babies eat mom’s skin (sort of like breast milk) R. Crypsis, warning colors, and toxins a. Crypsis (camouflage) b. Aposematic colors: having a character, such as color, sound, odor, or behavior, that advertises an organism’s toxic properties to potential predators S. Breathing in lissamphibians a. Lungs evolved in basal bony fishes long before they were ever used by tetrapods for breathing on land b. The original mechanism for inflating lungs in fish is called buccal pumping i. Lissamphibians retain buccal pumping but 2 valves are needed instead since they don’t have a diaphragm ii. Air can be expelled in different ways → exhalation pump, nostrils T. Water balance a. Lissamphibians do not drink water and are very prone to cutaneous water loss and an influx of water b. Pelvic patch i. Drink through their crotch c. Can reabsorb water from urine d. Waxy, lipid-derived coating on skin secreted by dermal glands e. Rest during dry times U. Lissamphibians are dying a. Affects humans → higher rates of malaria (mosquitoes) and leishmaniasis (sandflies) i. Since lissamphibia numbers are dwindling, insects are thriving causing us more disease

Lecture 1-4 Notes: Vertebrate Zoology | PDF

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