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lecture 1-phylum chordata
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Comparative Vertebrate Anatomy  
Lecture Notes 1 - Chordate Origins & Phylogeny

Comparative vertebrate anatomy - the study of structure, of the function of structure, & of the range of variation in structure & function among vertebrates:

Kingdom: Animal

Phylum: Chordata

Subphylum: Vertebrata

Vertebrate characteristics:

1 - notochord (at least in the embryo)

2 - pharynx with pouches or slits in wall (at least in the embryo)

3 - dorsal, hollow nervous system

4 - vertebral column

Used by permission of John W. Kimball

Notochord = rod of living cells ventral to central nervous system & dorsal to alimentary canal

Fate of notochord during development:

  • Head region - incorporated into floor of skull
  • Trunk & tail - surrounded by cartilaginous or bony vertebrate (except in Agnathans)


  • Fishes & amphibians - notochord persists the length of the trunk & tail but is constricted within the centrum of each vertebra
  • Reptiles, birds, & mammals - notochord almost disappears during development (e.g., remains as a pulpy nucleus in the vertebrae of mammals)
  • Protochordates - notochord remains as the chief axial skeleton
  • Agnathans - lateral neural cartilages are located on notochord lateral to the spinal cord

Pharynx - region of alimentary canal exhibiting pharyngeal pouches in embryo; pouches may open to the exterior as slits:

    • permanent slits - adults that live in water & breathe via gills
    • temporary slits - adults live on land

Dorsal, hollow central nervous system - consists of brain & spinal cord & contains a central cavity (called the neurocoel)

Vertebrate beginnings

Among the oldest & best known = ostracoderms

  • fishes that occurred in the late Cambrian period (see The Cambrian Explosion) through the Devonian (about 400 - 525 million years before present)
  • had bony plates and scales (&, therefore, were easily fossilized)
  • jawless vertebrates called 'armored fishes'

Before ostracoderms?


Before Vertebrates?

  • Cathaymyrus diadexus (literally the 'Chinese eel of good fortune') is not the fossil of an eel. At just 5 cm long, but 535 m.y. old, it is the earliest known chordate (fossil shown below; for a 'reconstruction' check Researchers think that Cathaymyrus is a fossil relative of modern lancelets (amphioxus).


Non-vertebrate chordates still alive today include tunicates (or sea squirts; urochordates) & amphioxus (or branchiostoma). (cephalochordates)

Phylum Chordata - established in 1874 & included organisms with:

1 - notochord

2 - pharyngeal pouches or slits

3 - dorsal, hollow nervous system

4 - cells that produce the hormone thyroxine  

Subphylum Urochordata = tunicates

Chordate 'ancestor' of vertebrates:

      • sessile (like adult tunicates)
      • tail evolved as adaptation in larvae to increase mobility
      • 'higher forms' - came about by retention of tail (neoteny)

Tunicate larva - also called 'sea squirt'

      • notochord is confined to the tail
      • notochord is lost during metamorphosis into sessile adult
      • possess pharyngeal slits


A 530 million-year-old (although perhaps as old as 560 million years) creature, Cheungkongella ancestralis, probably a tunicate, found in the Chengjiang fauna in China's southwest Yunnan Province, might be the earliest known fossil evidence of primitive chordates (Shu, D.-G., L. Chen, J. Han, X.-L. Zhang. 2001. An early Cambrian tunicate from China. Nature 411:472 - 473.)

Subphylum Cephalochordata= Amphioxus (or Branchiostoma)

Vertebrate features:

    • notochord
    • dorsal, hollow nervous system
    • pharyngeal gill slits
    • 'circulatory' system - vertebrate pattern with 'pumping vessels' (but no heart)

Hemichordates = acorn worms

Bateson added acorn worms to the phylum Chordata in 1884 because they have:

1 - a dorsal, hollow nervous system

2 - gill slits

3 - a short diverticulum of the gut called the stomochord

Present consensus = the stomochord is not homologous with the notochord and Hemichordates are placed in a separate phylum

Possible invertebrate ancestors:

1 - annelid worms  

Evidence for:
    • bilateral symmetry
    • segmented
    • central nervous system with brain  
      & longitudinal nerve cord
Evidence against:
    • nerve cord is solid
    • nerve cord is ventral

2 - echinodermata - chordate characteristics include:

    • radial cleavage - blastomeres in adjacent tiers lie directly above one another (as opposed to spiral cleavage)
    • anus forms near or at blastopore (deuterostomous)
    • mesoderm arises as outpocketing of the gut wall
    • indeterminate cleavage (i.e., fate of blastomeres isn't predetermined)

Phylum: Chordata  
Subphylum: Vertebrata  
Superclass: Pisces

Class Agnatha  
Class Placodermii  
Class Chondricthyes  
Class Acanthodii  
Class Osteichthyes

Superclass: Tetrapoda

Class Amphibia  
Class Reptilia  
Class Aves  
Class Mammalia

Agnathans vs. Gnathostomes:

  • semicircular canals
    • agnathans have 1 or 2
    • gnathostomes have 3
  • jointed, paired lateral appendages
  • jaws
    • agnathans have none
    • gnathostomes do

Class Agnatha


1 - Osteostraci

2 - Anaspida

3 - Thelodonti

4 - Galeaspida

5 - Pituriaspida

6 - Petromyzontia (lampreys)

7 - Myxinoidea (hagfishes)

Ostracoderms (Osteostraci, Anaspida, Heterostraci, & Coelolepid):

1 - extinct Paleozoic (Cambrian to Devonian) jawless fish with an external skeleton of bone ('bony armor')  
2 - oldest known vertebrates  
3 - many had flattened appearance (some may have been bottom-dwellers)

Cyclostomes (Petromyzontia & Myxinoidea):

Lampreys - parasitic with horny, rasping teeth (see drawing at right)

Hagfishes - primarily scavengers



1 - earliest known gnathostomes (Silurian; about 440 mybp)

2 - probably related to modern bony fishes

3 - small (less than 20 cm long) with large eyes

4 - Acanthodians most likely died out because of the rapidly increasing number of ray-finned fishes and sharks during the Permian

The relationships of acanthodians to other vertebrates has been the subject of considerable debate. Early researchers considered them to be most closely related to the ray-finned fishes, but most scientists during the mid-20th Century considered acanthodians to have a closer affinity to the sharks. Opinion has now generally swung back in favor of a closer relationship with ray-fins, but this is far from universally accepted.

Class Placodermii:

1 - Silurian (about 420 million years before present)

2 - probably off the main line of vertebrate evolution

3 - many had bony dermal shields

4 - some were probably predators (with large, sharp 'tooth plates')

Placoderms were armored jawed fishes that first appeared about 420 million years ago (MYA) during the Silurian Period. They had diversified dramatically by the beginning of the Devonian and came to dominate most marine and freshwater ecosystems before becoming extinct at the end of that period (355 MYA). About 200 genera of placoderms have been discovered, with most of these occurring during the Devonian radiations. The rapid evolution and diversity of placoderms have made them useful in dating Devonian rocks. Placoderms (= plated skin) were named for their heavy armor of dermal bone, which formed large shields on the head and thorax. The rest of their bodies was covered with small bony scales or was without dental armor. The head and trunk shields of most placoderms were articulated by bony joints. This joint apparently allowed the forward part of the skull to tilt up, increasing the gape. Placoderms lacked teeth, but biting or grinding structures are often be found in the dermal bones lining their mouths. Placoderms evolved into a variety of body forms in a relatively short time. Many were torpedo-shaped, but there were notable expections, including the flatten Phyllolepida and the bottom feeding Antiarchi. Most placoderms were less than 30 cm (2 feet) in length, but some members of the dinichthyids (= terrible fish) reached or exceeded 6 m (20 ft), making them the first giants of the vertebrate lineage.

Class Chondrichthyes - cartilaginous fishes

1 - ancestors had bony skeletons so cartilaginous skeleton is specialized

2 - pelvic fins of males are modified as claspers

3 - placoid scales

4 - numerous today but more abundant in the past

Subclass Elasmobranchii - most common cartilaginous fishes

O. Cladoselachii - primitive sharks (300-400 mybp)

O. Selachii - 'modern' sharks

O. Batoidea - rays & skates


1 - 1st pharyngeal slit modified as a spiracle

2 - naked gill slits (no operculum)

3 - mouth located ventrally  

Subclass Holocephali

O. Chimaeriformes (photo & drawing)

        • marine
        • gill slits have a fleshy operculum & the spiracle is closed
        • few scales
        • common ancestor with sharks but an independent line

Class Osteichthyes - bony fishes

1 - skeleton is partly or chiefly bone

2 - gill slits are covered by a bony operculum

3 - skin has scales with, typically, little bone

4 - most have a swim bladder

5 - ray-finned or lobe-finned

Subclass Actinopterygii - ray-fins

Superorder Chondrostei

        • most primitive ray-fins
        • chiefly Paleozoic (300-400 mybp)
        • include present-day Sturgeons & Paddlefish (below)

Superorder Neopterygii

Order Semionotiformes

          • dominant Mesozoic fishes
          • possess ganoid scales
          • two extant genera:
            • Lepidosteus - predatory; includes present-day gars
            • Amia - includes present-day bowfins (or dogfish)

Division Teleostei - modern ray-finned fishes

          • recent bony fishes
          • 95% of all living fish
          • about 40 living orders
          • well-ossified skeleton
          • cycloid & ctenoid scales (flexible & overlapping)
          • pelvic fins often located far forward
          • no spiracle

1 = operculum, 2 = dorsal fin, 3 = caudal peduncle (The narrow section of a fish's body directly  
anterior to the insertion of the tail but before the mid-body.), 4 = caudal fin or "tail", 5 = anal fins,  
6 = pelvic fins, & 7 = pectoral fins  

Subclass Sarcopterygii - lobe-finned fishes

O. Crossopterygii - chiefly Paleozoic except Latimeria  

1 - resemble early amphibians

2 - skeleton of fin lobe corresponds closely to proximal skeletal elements of early tetrapod limbs

Used with permission of John Kimball

3 - skull similar to that of early amphibians

4 - had swim bladders that may have been used as lungs

O. Dipnoi - lungfish (3 living genera; Africa, Australia, & South America)

        • African & South American species have inefficient gills & will drown if held under water
        • Australian species (Neoceratodus spp.) relies on gills unless oxygen content of water is too low

Class Amphibia

Oldest known = subclass Labyrinthodontia  

Fish-like features:

1- small bony scales in the skin

2- fin-rays in the tail (for swimming)

3- a skull similar to that of some Crossopterygians

4- a sensory canal system (like the lateral line system) that indicates a primarily aquatic existence

Labyrinthodonts are distinguished by deeply folded structure of enamel and dentine layers in the teeth, that look like an intricate labyrinth in the cross section, hence the name of this group. Labyrinthodonts were probably similar to fishes in their mode of living. Labyrinthodonts, like fishes and most modern amphibians, laid eggs in the water, where their larvae developed into mature animals. All labyrinthodonts had special sense organs in the skin, that formed a system for perception of water fluctuations. Moreover, some of them possessed well developed gills. In contrast, many labyrinthodonts seemingly had primitive lungs. They could breath atmospheric air, that was a great advantage for residents of warm shoals with low oxygen levels in the water. The air was inflated into the lungs by contractions of a special throat sac. Primitive members of all labyrinthodont groups were probably true water predators, and only advanced forms that arose independently in different groups and times, gained an amphibious, semi-aquatic mode of living. Mature individuals of advanced labyrinthodonts could live on land, feeding mainly on insects and other small invertebrates. Well ossified robust skeletons in some Late Carboniferous and Early Permian labyrinthodonts prove their adaptation to the terrestrial mode of life. It suggests that amphibians had successfully 'organized' actual terrestrial assemblages prior to the wide expansion of reptiles.

The most diverse group of the labyrinthodonts was the batrachomorphs ('similar to a frog'). Though these animals looked more like crocodiles, they most probably gave rise to the order Anura, the amphibians without tails, which include, in particular, the modern frogs. Batrachomorphs appeared in the Late Devonian, but they had worldwide distribution in the continental shallow basins of the Permian (Platyoposaurus, Melosaurus) and Triassic Periods (Thoosuchus, Benthosuchus, Eryosuchus). Some batrachomorphs existed until the end of the Cretaceous.

Subclass Lepospondyli

    • ancestry uncertain due to lack of fossil evidence
    • probably on a 'side branch' of vertebrate evolution

Subclass Lissamphibia - modern amphibians

O. Anura - frogs & toads  
O. Urodela - tailed amphibians  
O. Gymnophiona (apodans) - wormlike, burrowing amphibians

Modern amphibian characteristics:

1 - aquatic larval stage with external gills

2 - middle ear cavity with ear ossicle (columella)

3 - no bony scales (except apodans)

Class Reptilia - the first amniotes:

1 - scaly

2 - clawed

3 - large, yolk-laden, shell-covered eggs laid on land

Stem reptiles = Cotylosaurs (about 300 mybp)

Reptile Subclasses:

1 - Anapsida

O. Cotylosauria - stem reptiles  
O. Chelonia - turtles & tortoises

        • unchanged for about 175 million years
        • identified by bony dermal plates to which ribs & trunk vertebrae are fused

2 - Lepidosauria

O. Rhynchocephalia (Sphenodonta) - only living representative is the Tuatara  
O. Squamata - lizards, geckos, & snakes

3 - Archosauria

O. Thecodontia - stem archosaurs  
O. Pterosauria (check this short video & this one)  
O. Saurischia - 2 major groups: sauropods & theropods (check this short video)  
O. Ornithischia (like Iguanodon)  
O. Crocodilia

4 - Euryapsida - marine reptiles, includes the plesiosaurs (check this short video) & ichthyosaurs (check this short video)

Representative ichthyosaurs  

5 - Synapsida

O. Pelycosauria - first stage in evolution to mammals  
O. Therapsida

Saurischia (sawr-RIS-kee-ah) & Ornithischia are the two orders of dinosaurs, with the division based on the shape of the pelvic bone. The saurischian pubis (left) juts forward, and its ischium points backward. The ornithischian pubis and ischium (right) both point backward. The ornithischians were all herbivorous, and included some of the most interesting-looking dinosaurs. Ornithischian dinosaurs include three suborders: Ornithopoda, Marginocephalia and Thyreophora. The famous carnivorous dinosaurs were from the saurischian order, as were the largest herbivorous dinosaurs. The saurischian dinosaurs include two suborders: Theropoda and Sauropodomorpha.

The first vertebrates to evolve true flight were the pterosaurs, flying archosaurian reptiles. After the discovery of pterosaur fossils in the 18th century, it was thought that pterosaurs were a failed experiment in flight; a humorous mishap; or that they were simply gliders, too weak to fly. More recent studies have revealed that pterosaurs were definitely proficient flyers, and were no evolutionary failure; as a group they lasted about 140 million years (about as long as birds have)! Pterosaurs are thought to be derived from a bipedal, cursorial (running) archosaur in the late Triassic period (about 225 million years ago). No other phylogenetic hypothesis has withstood examination; however, the early history of pterosaurs is not yet fully understood because of their poor fossil record in the Triassic period. We can infer that the origin of flight in pterosaurs fits the "ground up" evolutionary scenario, supported by the fact that pterosaurs had no evident arboreal adaptations.

The pterosaur wing was supported by an elongated fourth digit (imagine having a "pinky finger" several feet long, and using that to fly!). Pterosaurs had other morphological adaptations for flight as a keeled sternum for the attachment of flight muscles, a short and stout humerus (the first arm bone), and hollow but strong limb and skull bones. Pterosaurs also had modified scales that were wing-supporting fibers, and that possibly formed hairlike structures to provide insulation -- bird feathers are analogous to the wing fibers of pterosaurs, and both are thought to possibly have been evolved originally for the primary purpose of thermoregulation (which implies, but does not prove, that both pterosaurs and the earliest birds were endothermic).

Early pterosaurs (such as Dimorphodon) had long tails that assisted balance, but later pterosaurs had no tails, and may have been more adept flyers. The most derived pterosaurs, such as Pteranodon and Quetzalcoatlus, were so large that soaring was the only feasible option; these were the largest flyers ever to cast a shadow on the Earth's surface.

Reptile subclasses - classified in part according to presence or absence of temporal openings

  • Synapsid type = mammal-like reptiles
  • Anapsid type = stem reptiles & turtles
  • Diapsid type = rhynchocephalians, lizards, & snakes
  • Euryapsid type = extinct plesiosaurs.

Temporal fenestration has long been used to classify amniotes. Taxa such as Anapsida, Diapsida, Euryapsida, and Synapsida were named after their type of temporal fenestration. Temporal fenestra are large holes in the side of the skull. The function of these holes has long been debated. Many believe that they allow muscles to expand and to lengthen. The resulting greater bulk of muscles results in a stronger jaw musculature, and the longer muscle fibers allow an increase in the gape.

Class Aves - birds

1 - may have arisen from an archosaurian reptile, perhaps a small bipedal dinosaur

2 - lost several dinosaur characteristics (e.g., long tail & teeth) but retained others (e.g., claws, scales, diapsid skull, single occipital condyle &, perhaps, feathers) (see AMNH website & ABC News website)

Subclass Archaeornithes

Genera: Archaeopteryx & Archaeornis


1 - solid bones

2 - weakly developed keel &, probably, weakly developed flight muscles

Subclass Neornithes

Superorder Odontognathae

      • extinct
      • many features of modern birds (e.g., hollow bones & short tail)

Superorder Paleognathae

      • ratites
      • small wings but powerful leg muscles

Superorder Neognathae - birds adapted for sustained flight  

Modifications to reduce weight include:

        • loss of some bones
        • pneumatic bones
        • reduced tail
        • loss of teeth
        • loss of urinary bladder

Class Mammalia


1 - hair  
2 - mammary glands  
3 - 3 middle ear bones  
4 - muscular diaphragm  
5 - sweat glands  
6 - marrow within bones  
7 - 2 sets of teeth  
8 - biconcave, enucleate red blood cells  
9 - well-developed cerebral cortex

Subclass Prototheria - egg-laying mammals

O. Monotremata - platypus + 2 spiny anteaters

1 - lay eggs  
2 - testes within the abdominal cavity  
3 - no pinna  
4 - no corpus callosum  
5 - less stable body temperature

Subclass Theria

Infraclass Metatheria

O. Marsupialia - pouched mammals; young born alive, but at a very immature stage

Infraclass Eutheria - placental mammals

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